In situ isolation of nuclei or nuclear proteins from adherent cells: a simple, effective method with less cytoplasmic contamination.

BACKGROUND: Isolation of nuclei or nuclear proteins is a prerequisite for western blot, nuclear proteome profiling, and other evaluations of nuclear proteins. Here, we developed a simple method for in situ isolation of nuclei or nuclear proteins by in situ removing the extranuclear part of adherent cells via a classical nonionic detergent triton X-100. RESULTS: First, the feasibility of our method was confirmed by confocal microscopy, atomic force microscopy, scanning electron microscopy, dynamic light scattering, immunofluorescence imaging, and time-lapse dynamic observation. Next, the optimal concentration range (approximately 0.1-1% for ~ 10 min) of triton X-100 and the optimal treatment time (< 30 min) of 0.1-1% Triton X-100 for our method were determined via western blotting of eight extra-/intra-nuclear proteins. Subsequently, the effectiveness, sensitivity, and cytoplasmic contamination of our method were tested by investigating the levels of phosphorylated p65 (a NF-κB subunit) in the nuclei of endothelial or tumor cells treated with/without lipopolysaccharide (LPS) via western blotting and by comparing with a commercial nuclear protein extraction kit (a classical detergent-based method). The data show that compared with the commercial kit our method obtained a higher yield of total nuclear proteins, a higher pP65 level in both control and LPS groups, and much lower content of GAPDH (as a reference for cytoplasmic contamination) in nuclei. CONCLUSIONS: The in situ isolation of nuclei or nuclear proteins from adherent cells in this study is a simple, effective method with less cytoplasmic contamination. This method/strategy has the potential of improving the quality of downstream evaluations including western blotting and proteomic profiling.

High-density adherent culture of CHO cells using rolled scaffold bioreactor.

Rapid expansion of biopharmaceutical market calls for more efficient and reliable platforms to culture mammalian cells on a large scale. Stirred-tank bioreactors have been widely used for large-scale cell culture. However, it requires months of trials and errors to optimize culture conditions for each cell line. In this article, we extend our earlier studies on rolled scaffold (RS) bioreactors for high-density adherent cell culture and report two new implementations of RSs with greatly enhanced mass-manufacturability, termed as Mesh-RS and Fiber-RS. CHO-K1 cells were successfully expanded in Mesh-RS and Fiber-RS bioreactors with an average growth rate of 1.09 ± 0.04 1/day and 0.95 ± 0.07 1/day, which were higher than those reported in similar studies. Fiber-RS bioreactor exhibited a very high cell density of 72.8 × 106 cells/ml. Besides, a dialyzer was integrated into the RS bioreactor to remove cellular waste and to replenish nutrients without disturbing the cells. By collecting the dialyzed media separately, the dialysis efficiency was significantly improved. In conclusion, the developed RS bioreactor has a strong potential to provide a highly reliable and easily scalable platform for large-scale cell culture in the biopharmaceutical industry.

[Development of a culture chamber for mechanical loading of adherent cells with large uniform strain].

Based on the current study of the influence of mechanical factors on cell behavior which relies heavily on experiments in vivo, a culture chamber with a large uniform strain area containing a linear motor-powered, up-to-20-Hz cell stretch loading device was developed to exert mechanical effects on cells. In this paper, using the strain uniformity as the target and the substrate thickness as the variable, the substrate bottom of the conventional incubation chamber is optimized by using finite element technique, and finally a new three-dimensional model of the incubation chamber with "M" type structure in the section is constructed, and the distribution of strain and displacement fields are detected by 3D-DIC to verify the numerical simulation results. The experimental results showed that the new cell culture chamber increased the accuracy and homogeneous area of strain loading by 49.13% to 52.45% compared with that before optimization. In addition, the morphological changes of tongue squamous carcinoma cells under the same strain and different loading times were initially studied using this novel culture chamber. In conclusion, the novel cell culture chamber constructed in this paper combines the advantages of previous techniques to deliver uniform and accurate strains for a wide range of cell mechanobiology studies.

Modelling and Differential Quantification of Electric Cell-Substrate Impedance Sensing Growth Curves.

Measurement of cell surface coverage has become a common technique for the assessment of growth behavior of cells. As an indirect measurement method, this can be accomplished by monitoring changes in electrode impedance, which constitutes the basis of electric cell-substrate impedance sensing (ECIS). ECIS typically yields growth curves where impedance is plotted against time, and changes in single cell growth behavior or cell proliferation can be displayed without significantly impacting cell physiology. To provide better comparability of ECIS curves in different experimental settings, we developed a large toolset of R scripts for their transformation and quantification. They allow importing growth curves generated by ECIS systems, edit, transform, graph and analyze them while delivering quantitative data extracted from reference points on the curve. Quantification is implemented through three different curve fit algorithms (smoothing spline, logistic model, segmented regression). From the obtained models, curve reference points such as the first derivative maximum, segmentation knots and area under the curve are then extracted. The scripts were tested for general applicability in real-life cell culture experiments on partly anonymized cell lines, a calibration setup with a cell dilution series of impedance versus seeded cell number and finally IPEC-J2 cells treated with 1% and 5% ethanol.

Dancing with the Cells: Acoustic Microflows Generated by Oscillating Cells.

The interaction of a sound or ultrasound wave with an elastic object, such as a microbubble, can give rise to a steady-state microstreaming flow in its surrounding liquid. Many microfluidic strategies for cell and particle manipulation, and analyte mixing, are based on this type of flow. In addition, there are reports that acoustic streaming can be generated in biological systems, for instance, in a mammalian inner ear. Here, new observations are reported that individual cells are able to induce microstreaming flow, when they are excited by controlled acoustic waves in vitro. Single adherent cells are exposed to an acoustic field inside a microfluidic device. The cell-induced microstreaming is then investigated by monitoring flow tracers around the cell, while the structure and extracellular environment of the cell are altered using different chemicals. The observations suggest that the maximum streaming flow induced by an MDA-MB-231 breast cancer cell can reach velocities on the order of mm s-1 , and this maximum velocity is primarily governed by the overall cell stiffness. Therefore, such cell-induced microstreaming measurements, including flow pattern and velocity magnitude, may be used as label-free proxies of cellular mechanical properties, such as stiffness.

A "No-Touch" Antibody-Staining Method of Adherent Cells for High-Throughput Flow Cytometry in 384-Well Microplate Format for Cell-Based Drug Library Screening.

In the last decade, screening compound libraries on live cells has become an important step in drug discovery. The abundance of compounds in these libraries requires effective high-throughput (HT) analyzing methods. Although current cell-based assay protocols are suitable for HT analyses, the analysis itself is often restrained to simple, singular outcomes. Incorporation of HT samplers on flow cytometers has provided an interesting approach to increase the number of measurable parameters and increase the sensitivity and specificity of analyses. Nonetheless, to date, the labor intensive and time-consuming strategies to detach and stain adherent cells before flow cytometric analysis has restricted use of HT flow cytometry (HTFC) to suspension cells. We have developed a universal "no-touch" HTFC antibody staining protocol in 384-well microplates to bypass washing and centrifuging steps of conventional flow cytometry protocols. Optimizing culture conditions, cell-detachment and staining strategies in 384-well microplates resulted in an HTFC protocol with an optimal stain index with minimal background staining. The method has been validated using six adherent cell lines and simultaneous staining of four parameters. This HT screening protocol allows for effective monitoring of multiple cellular markers simultaneously, thereby increasing informativity and cost-effectiveness of drug screening. © 2019 The Authors. Cytometry Part A published by Wiley Periodicals LLC. on behalf of International Society for Advancement of Cytometry.

Fast and ergonomic extraction of adherent mammalian cells for NMR-based metabolomics studies.

Cellular metabolomics has become key to elucidate mechanistic aspects in various fields such as cancerology or pharmacology, and is rapidly becoming a standard phenotyping tool accessible to the broad biological community. Acquisition of reliable spectroscopic datasets, such as nuclear magnetic resonance (NMR) spectra, to characterize biological systems depends on the elaboration of robust methods for cellular metabolites extraction. Previous studies have addressed many issues raised by these protocols, however with little pondering on ergonomic and practical aspects of the methods that impact their scalability, reproducibility and hence their suitability to high-throughput studies or their use by non-metabolomics experts. Here, we optimize a fast and ergonomic protocol for extraction of metabolites from adherent mammalian cells for NMR metabolomics studies. The proposed extraction protocol, including cell washing, metabolism quenching and actual extraction of intracellular metabolites, was first optimized on HeLa cells. Efficiency of the protocol, in its globality and for the different individual steps, was assessed by NMR quantification of 27 metabolites from cellular extracts. We show that a single PBS wash provides a seemly compromise between contamination from growth medium and leakage of intracellular metabolites. In HeLa cells, extraction using pure methanol, without cell scraping, recovered a higher amount of intracellular metabolites than the reference methanol/water/chloroform method with cell scraping, with yields varying across metabolite classes. Optimized and reference protocols were further tested on eight cell lines of miscellaneous nature, and inter-operator reproducibility was demonstrated. Our results stress the need for tailored extraction protocols and show that fast protocols minimizing time-consuming steps, without compromising extraction yields, are suitable for high-throughput metabolomics studies. Graphical abstract.

Combining fluorescent cell barcoding and flow cytometry-based phospho-ERK1/2 detection at short time scales in adherent cells.

Detection of levels of intracellular phospho-proteins is key to analyzing the dynamics of signal transduction in cellular systems. Cell-to-cell variability in the form of differences in protein level in each cell affects signaling and is implicated in prognosis of many diseases. Quantitative analysis of such variability necessitate measuring the protein levels at single-cell resolution. Single-cell intracellular protein abundance detection in statistically significant number of adherent cells for short time sampling points post stimulation using classical flow cytometry (FCM) technique has thus far been a challenge due to the detrimental effects of cell detachment methods on the cellular machinery. We systematically show that cell suspension obtained by noninvasive temperature-sensitive detachment of adherent cells is amenable to high-throughput phospho-ERK1/2 protein detection at single-cell level using FCM in these short time sampling points. We demonstrate this on three adherent cell lines, viz., HeLa, A549, and MCF7, from distinct lineages having characteristically different elasticity at 37 °C. In particular, we use a right combination of multiplexing via fluorescent cell barcoding (FCB) and intracellular antibody staining for simultaneous detection of phospho-ERK1/2 (pERK) stimulated by epidermal growth factor (EGF) in multiple samples. Based on systematic characterization using Alexa 350 dye, we arrive at two conditions that must be satisfied for correct implementation of FCB. Our study reveals that the temperature-sensitive detachment of HeLa cells correctly captures the expected pronounced bimodal pERK distribution as an early response to EGF, which the enzymatic treatment methods fail to detect. © 2018 International Society for Advancement of Cytometry.

Role of psl Genes in Antibiotic Tolerance of Adherent Pseudomonas aeruginosa.

Bacteria attached to a surface are generally more tolerant to antibiotics than their planktonic counterparts, even without the formation of a biofilm. The mechanism of antibiotic tolerance in biofilm communities is multifactorial, and the genetic background underlying this antibiotic tolerance has not yet been fully elucidated. Using transposon mutagenesis, we isolated a mutant with reduced tolerance to biapenem (relative to that of the wild type) from adherent cells. Sequencing analysis revealed a mutation in the pslL gene, which is part of the polysaccharide biosynthesis operon. The Pseudomonas aeruginosa PAO1ΔpslBCD mutant demonstrated a 100-fold-lower survival rate during the exposure of planktonic and biofilm cells to biapenem; a similar phenotype was observed in a mouse infection model and in clinical strains. Transcriptional analysis of adherent cells revealed increased expression of both pslA and pelA, which are directly regulated by bis-(3',5')-cyclic dimeric GMP (c-di-GMP). Inactivation of wspF resulted in significantly increased tolerance to biapenem due to increased production of c-di-GMP. The loss of pslBCD in the ΔwspF mutant background abolished the biapenem-tolerant phenotype of the ΔwspF mutant, underscoring the importance of psl in biapenem tolerance. Overexpression of PA2133, which can catalyze the degradation of c-di-GMP, led to a significant reduction in biapenem tolerance in adherent cells, indicating that c-di-GMP is essential in mediating the tolerance effect. The effect of pslBCD on antibiotic tolerance was evident, with 50- and 200-fold-lower survival in the presence of ofloxacin and tobramycin, respectively. We speculate that the psl genes, which are activated by surface adherence through elevated intracellular c-di-GMP levels, confer tolerance to antimicrobials.

Explorative gene analysis of antibiotic tolerance-related genes in adherent and biofilm cells of Pseudomonas aeruginosa.

BACKGROUND: Antibiotic tolerance has attracted worldwide attention, as it leads to chronic, refractory, and persistent infections that are difficult to control. Bacterial biofilms are well known to be more tolerant to antibiotics compared to planktonic bacteria. We previously revealed that adherent bacteria on a solid surface also exhibited tolerance to antibiotics before forming a biofilm. However, little is known about the mechanisms of antibiotic tolerance for adherent or biofilm cells. OBJECTIVES: We investigated the mechanisms of antibiotic tolerance in the biofilm life cycle using adherent and biofilm cells, and evaluated the possibility that common mechanisms operate at each stage. METHODS: We constructed transposon mutants of Pseudomonas aeruginosa PAO1 and screened for low-tolerant mutants with two different methods, using adherent cells and biofilm cells. RESULTS: Fourteen and nine mutants exhibiting low antibiotic tolerance were detected in the adherent cells and biofilm cells, and 14 and 7 candidate genes linked to this tolerance were identified by sequencing, respectively. Eight of the 14 genes related to the antibiotic tolerance of the adherent cells were involved in biofilm formation. Two of the seven genes related to the antibiotic tolerance of biofilm cells participated in the antibiotic tolerance of adherent cells. CONCLUSIONS: The antibiotic tolerance of adherent cells and biofilm formation appear to be under the same regulation mechanism to promote survival in the presence of antibiotics. Antibiotic tolerance shows a complex regulation mechanism at each stage of biofilm formation.

Optimization of nanofibrous silk fibroin scaffold as a delivery system for bone marrow adherent cells: in vitro and in vivo studies.

Electrospun silk fibroin nanofibrous scaffolds (ESFNSs) were successfully prepared by electrospinning of various Bombyx mori silk fibroin concentrations (10, 12, and 14% in formic acid). After characterizing the purified silk fibroin, the morphology, porosity, fibers' diameter, and uniformity of the prepared scaffolds were examined in detail. In addition, biological responses such as effects on bone marrow cell viability, cytotoxicity, and cell adhesion were evaluated in vitro. Biocompatibility and bioactivity properties of the ESFNSs were evaluated in vitro and in vivo by cell culturing and subcutaneous implantation in rat models for 7 and 28 days, respectively. According to the obtained results, no beaded fibers were seen in any of the prepared scaffolds, whereas ESFNS-10% provided more uniformity and porosity with nanoscaled fibers (90 ± 0.021 nm). Furthermore, the scaffolds also showed good cell adhesion and spreading (68.7 ± 11.8 and 7.6 ± 3.3 total length and width, respectively) with no detectable effect on cell viability and cytotoxicity. The in vivo biocompatibility evaluation indicated that the scaffolds did not stimulate detectable cellular inflammatory response (lymphocytes) and increased the total cell number (cellularity) in the implantation area. Furthermore, the results suggest the potential use of the prepared ESFNS-10% bone marrow cell constructs in direct implantation for tissue engineering applications.

Temperature-induced labelling of Fluo-3 AM selectively yields brighter nucleus in adherent cells.

Fluo-3 is widely used to study cell calcium. Two traditional approaches: (1) direct injection and (2) Fluo-3 acetoxymethyl ester (AM) loading, often bring conflicting results in cytoplasmic calcium ([Ca(2+)]c) and nuclear calcium ([Ca(2+)]n) imaging. AM loading usually yields a darker nucleus than in cytoplasm, while direct injection always induces a brighter nucleus which is more responsive to [Ca(2+)]n detection. In this work, we detailedly investigated the effects of loading and de-esterification temperatures on the fluorescence intensity of Fluo-3 in response to [Ca(2+)]n and [Ca(2+)]c in adherent cells, including osteoblast, HeLa and BV2 cells. Interestingly, it showed that fluorescence intensity of nucleus in osteoblast cells was about two times larger than that of cytoplasm when cells were loaded with Fluo-3 AM at 4 °C and allowed a subsequent step for de-esterification at 20 °C. Brighter nuclei were also acquired in HeLa and BV2 cells using the same experimental condition. Furthermore, loading time and adhesion quality of cells had effect on fluorescence intensity. Taken together, cold loading and room temperature de-esterification treatment of Fluo-3 AM selectively yielded brighter nucleus in adherent cells.

Automated method for the rapid and precise estimation of adherent cell culture characteristics from phase contrast microscopy images.

The quantitative determination of key adherent cell culture characteristics such as confluency, morphology, and cell density is necessary for the evaluation of experimental outcomes and to provide a suitable basis for the establishment of robust cell culture protocols. Automated processing of images acquired using phase contrast microscopy (PCM), an imaging modality widely used for the visual inspection of adherent cell cultures, could enable the non-invasive determination of these characteristics. We present an image-processing approach that accurately detects cellular objects in PCM images through a combination of local contrast thresholding and post hoc correction of halo artifacts. The method was thoroughly validated using a variety of cell lines, microscope models and imaging conditions, demonstrating consistently high segmentation performance in all cases and very short processing times (<1 s per 1,208 × 960 pixels image). Based on the high segmentation performance, it was possible to precisely determine culture confluency, cell density, and the morphology of cellular objects, demonstrating the wide applicability of our algorithm for typical microscopy image processing pipelines. Furthermore, PCM image segmentation was used to facilitate the interpretation and analysis of fluorescence microscopy data, enabling the determination of temporal and spatial expression patterns of a fluorescent reporter. We created a software toolbox (PHANTAST) that bundles all the algorithms and provides an easy to use graphical user interface. Source-code for MATLAB and ImageJ is freely available under a permissive open-source license.

In-vitro Behavior of Human Umbilical Cord Blood Stem Cells Towards Serum Based Minimal Cytokine Growth Conditions.

We tried here to optimize the proliferation of both Hematopoietic and Mesenchymal stem cells of Umbilical Cord blood in minimal cytokine growth condition. Failing to get good results of expansion of non-adherent Hematopoietic Total Nucleated Cells and adherent Fibroblastic Mesenchymal Stem Cells derived from 10-12 ml of collected Cord blood, we designed the further experimental study by increasing the volume of Cord blood sample up to 65-70 ml. We harvested the non-adherent as well as adherent fraction separately derived from the primary culture of Umbilical Cord blood stem cells under the influence of growth promoting Cytokines or Growth Factors. The proliferation study was conducted by taking different combinations of two hematopoietic growth stimulatory Cytokines like stem cell factor (SCF) and Fms like tyrosine kinase-3Ligand (Flt3L) at concentrations (10 ng/ml, 100 ng/ml) while we preferred Mesenchymal specific growth factor i.e. basic Fibroblast growth factor (FGF-ß) at its 10 ng/ml concentration for adherent cells to get optimal results. The Hematopoietic and Fibroblast Colony forming abilities of the expanded stem cells were performed through Colony Forming Unit assay. Culture Medium containing cytokine combination like SCF 100 ng/ml with Flt3L 10 ng/ml was found to be optimal for the proliferation of hematopoietic stem cells. But the number of hematopoietic colonies like Erythroid colonies generated were less in case of media supplemented with SCF & Flt3L while more number of Myeloid colonies were observed in Growth factor supplemented media in comparison to the control one. The FGF-ß supplemented media successfully enhanced the proliferation of Mesenchymal Stem Cells and exhibited its efficient Fibroblast colony forming ability. Our experimental study supports the minimal utilization of cytokines for haematopoietic and mesenchymal stem cell proliferation which may help in future safe Cord blood stem cell infusion.

PATrans: Pixel-Adaptive Transformer for edge segmentation of cervical nuclei on small-scale datasets.

Transformer has shown excellent performance in various visual tasks, making its application in medicine an inevitable trend. Nevertheless, simply using transformer for small-scale cervical nuclei datasets will result in disastrous performance. Scarce nuclei pixels are not enough to compensate for the lack of CNNs-inherent intrinsic inductive biases, making transformer difficult to model local visual structures and deal with scale variations. Thus, we propose a Pixel Adaptive Transformer(PATrans) to improve the segmentation performance of nuclei edges on small datasets through adaptive pixel tuning. Specifically, to mitigate information loss resulting from mapping different patches into similar latent representations, Consecutive Pixel Patch (CPP) embeds rich multi-scale context into isolated image patches. In this way, it can provide intrinsic scale invariance for 1D input sequences to maintain semantic consistency, allowing the PATrans to establish long-range dependencies quickly. Futhermore, due to the existing handcrafted-attention is agnostic to the widely varying pixel distributions, the Pixel Adaptive Transformer Block (PATB) effectively models the relationships between different pixels across the entire feature map in a data-dependent manner, guided by the important regions. By collaboratively learning local features and global dependencies, PATrans can adaptively reduce the interference of irrelevant pixels. Extensive experiments demonstrate the superiority of our model on three datasets(Ours, ISBI, Herlev).

Microplate-Based Cryopreservation of Adherent-Cultured Human Cell Lines Using Amino Acids and Proteins.

With the progression of regenerative medicine and cell therapy, the importance of cryopreservation techniques for cultured cells continues to rise. Traditional cryoprotectants, such as dimethyl sulfoxide and glycerol, are effective in cryopreserving suspended cells, but they do not demonstrate sufficient efficacy for two-dimensional (2D)-cultured cells. In the past decade, small molecules and polymers have been studied as cryoprotectants. Some L-amino acids have been reported to be natural and biocompatible cryoprotectants. However, the cryoprotective effects of D-amino acids have not been investigated for such organized cells. In the present study, the cryoprotective effects of D- and L-amino acids and previously reported cryoprotectants were assessed using HepG2 cells cultured on a microplate without suspending the cells. d-Proline had the highest cryoprotective effect on 2D-cultured cells. The composition of the cell-freezing solution and freezing conditions were then optimized. The d-proline-containing cell-freezing solution also effectively worked for other cell lines. To minimize the amount of animal-derived components, fetal bovine serum in the cell freezing solution was substituted with bovine serum albumin and StemFit (a commercial supplement for stem cell induction). Further investigations on the mechanism of cryopreservation suggested that d-proline protected enzymes essential for cell survival from freeze-induced damage. In conclusion, an effective and xeno-free cell-freezing solution was produced using d-proline combined with dimethyl sulfoxide and StemFit for 2D-cultured cells.

Analysis of the Adherent Cell Response to the Substrate Stiffness Using Tensegrity.

Cell's shape is dependent on the cytoskeleton mechanical properties. Hybrid models were developed that combine the discrete structure for the cytoskeleton and continuum parts for other cell organelles. Tensegrity-based structures that consist of tensile and compression elements are useful models to understand the cytoskeleton mechanical behavior. In this study, we are looking to examine the reaction of the cell to a variety of substrate stiffnesses and explain the relationship between cell behavior and substrate mechanical properties. However, which tensegrity structure is appropriate for modeling a living cell? Is the structure's complexity play a major role? We used two spherical tensegrities with different complexities to assess the impact of the structure on the cell's mechanical response versus substrate's stiffness. Six- and twelve-strut tensegrities together with membrane, cytoplasm, nucleoskeleton, and nucleus envelope were assembled in Abaqus package to create a hybrid cell model. A compressive load was applied to the cell model and the reaction forces versus deflection curves were analyzed for number of substrate stiffness values. By analyzing the difference due to two different tensegrities it became clear that the lower density structure is a better choice for modeling stiffer cells. It was also found that the six-strut tensegrity is sensitive to higher range of substrate stiffness.

A novel method for high-pressure freezing of adherent cells for frozen hydrated sectioning and CEMOVIS.

With the development of Cryo Electron Microscopy Of Vitreous Sections (CEMOVIS), imaging cells in a close to native state has become a reality. However with the commonly used carriers for high-pressure freezing and cryo-sectioning, adherent grown cells either need to be detached from their substrate. Here a new method is presented for high-pressure freezing adherent growing cells for frozen-hydrated sectioning and CEMOVIS. Cells are cultured on golden grids, containing a carbon coated Formvar film, and frozen on a membrane carrier which provides the grids with the structural support needed to withstand the strain of trimming and cryo-sectioning. This method was successfully tested for the two different types of high-pressure freezers, those using a pressure chamber (HPM010, EMHPF, Wohlwend Compact 01/02, HPM100) and those directly pressurizing the sample (EMPact series).

SFAlab: image-based quantification of mechano-active ventral actin stress fibers in adherent cells.

Ventral actin stress fibers (SFs) are a subset of actin SFs that begin and terminate at focal adhesion (FA) complexes. Ventral SFs can transmit forces from and to the extracellular matrix and serve as a prominent mechanosensing and mechanotransduction machinery for cells. Therefore, quantitative analysis of ventral SFs can lead to deeper understanding of the dynamic mechanical interplay between cells and their extracellular matrix (mechanoreciprocity). However, the dynamic nature and organization of ventral SFs challenge their quantification, and current quantification tools mainly focus on all SFs present in cells and cannot discriminate between subsets. Here we present an image analysis-based computational toolbox, called SFAlab, to quantify the number of ventral SFs and the number of ventral SFs per FA, and provide spatial information about the locations of the identified ventral SFs. SFAlab is built as an all-in-one toolbox that besides analyzing ventral SFs also enables the identification and quantification of (the shape descriptors of) nuclei, cells, and FAs. We validated SFAlab for the quantification of ventral SFs in human fetal cardiac fibroblasts and demonstrated that SFAlab analysis i) yields accurate ventral SF detection in the presence of image imperfections often found in typical fluorescence microscopy images, and ii) is robust against user subjectivity and potential experimental artifacts. To demonstrate the usefulness of SFAlab in mechanobiology research, we modulated actin polymerization and showed that inhibition of Rho kinase led to a significant decrease in ventral SF formation and the number of ventral SFs per FA, shedding light on the importance of the RhoA pathway specifically in ventral SF formation. We present SFAlab as a powerful open source, easy to use image-based analytical tool to increase our understanding of mechanoreciprocity in adherent cells.

Challenges in Mesenchymal Stromal Cell-based Therapies.

Over 50 years have passed since discovering mesenchymal stromal cells (MSCs). Initially, despite gaps in the knowledge of the identity of these cells, their therapeutic aspects were recognized. Consequently, MSCs became candidates for treating a wide range of diseases. However, the therapeutic effects of MSCs are not stable in the long term, and there are inconsistent data on their clinical efficacy. Even though more than 1000 MSC-based clinical trials have been registered, and the safety of MSCbased cell therapies has been proven, data on the clinical efficacy of MSCs have not been enough to warrant FDA approval for clinical treatment and marketing purposes. The available information on MSCs still contains some controversies, perhaps owing to little progress in understanding their in vivo identity. MSCs have been used for therapeutic purposes despite poor knowledge of their in vivo origin or functions. Hence, perhaps we need to go back to the basics of MSCs and spend more time understanding the biology of these cells. An improved understanding of MSCs' location and function within tissues may improve their therapeutic efficacy and, consequently, their establishment as a cell therapy product.