A beginner's guide to rigor and reproducibility in fluorescence imaging experiments

Geometrically constrained cytoskeletal reorganisation modulates DNA nanostructures uptake

DNA nanostructures (DNs) have gained popularity in various biomedical applications due to their unique properties, including structural programmability, ease of synthesis and functionalization, and low cytotoxicity. Effective utilization of DNs in biomedical applications requires a fundamental understanding of their interactions with living cells and the mechanics of cellular uptake. Current knowledge primarily focuses on how the physicochemical properties of DNs, such as mass, shape, size, and surface functionalization, affect uptake efficacy. However, the role of cellular mechanics and morphology in DN uptake remains largely unexplored. In this work, we show that cells subjected to geometric constraints remodel their actin cytoskeleton, resulting in differential mechanical force generation that facilitates DN uptake. The length, number, and orientation of F-actin fibers are influenced by these constraints, leading to distinct mechanophenotypes. Overall, DN uptake is governed by F-actin forces arising from filament reorganisation under geometric constraints. These results underscore the importance of actin dynamics in the cellular uptake of DNs and suggest that leveraging geometric constraints to induce specific cell morphology adaptations could enhance the uptake of therapeutically designed DNs.

A murine model of Trypanosoma brucei-induced myocarditis and cardiac dysfunction

Trypanosoma brucei is a protozoan parasite that causes human and animal African trypanosomiases (HAT and AAT). Cardiac symptoms are commonly reported in HAT patients, and intracardiac parasites with accompanying myocarditis have been observed in both natural hosts and animal models of T. brucei infection. Despite the importance of T. brucei as a cause of cardiac dysfunction and the dramatic socioeconomic impact of African trypanosomiases in sub-Saharan Africa, there are currently no reproducible murine models of T. brucei-associated cardiomyopathy. We present the first clinically relevant, reproducible murine model of cardiac dysfunction in chronic T. brucei infection. Similar to humans, mice showed histological evidence of myocarditis and elevation of serum NT-proBNP with electrocardiographic abnormalities. Serum NT-proBNP levels were elevated prior to the development of severe ventricular dysfunction. On flow cytometry, myocarditis was associated with an increase of most myocardial immune cell populations, including multiple T cell and macrophage subsets, corroborating the notion that T. brucei-associated cardiac damage is an immune-mediated event. This novel mouse model represents a powerful and practical tool to investigate the pathogenesis of T. brucei-mediated heart damage and supports the development of therapeutic options for T. brucei-associated cardiac disease. In characterizing this model, we provide evidence that T. brucei causes cardiac disease, and we suggest that immunopathology is an important contributor to cardiac pathology. Along with other recent studies, our work demonstrates the importance of extravascular spaces, including the heart, for T. brucei pathogenesis.

IMPORTANCE

African trypanosomiasis is a neglected tropical disease affecting both people and cattle, which represents a major public health problem in sub-Saharan Africa with an enormous socioeconomic impact. Cardiac disease represents an underappreciated clinical manifestation of African trypanosomiasis that may lead to lifelong illness despite successful treatment of infection. However, this aspect of African trypanosomiasis remains poorly understood, partially due to a lack of well-characterized and practical animal models. In this study, we present the development and characterization of a novel, reproducible, and cost-effective mouse model of cardiac dysfunction in African trypanosomiasis. We demonstrate that this model recapitulates major features of cardiac dysfunction in natural infection, including the presence of parasites in the cardiac interstitial spaces, alterations of cardiac biomarkers, and functional changes. This model represents a resource to support the understanding of cardiac complications of trypanosomiasis and the development of new therapies to prevent and treat cardiac involvement in African trypanosomiasis.

Tissue spaces are reservoirs of antigenic diversity for Trypanosoma brucei

The protozoan parasite Trypanosoma brucei evades clearance by the host immune system through antigenic variation of its dense variant surface glycoprotein (VSG) coat, periodically 'switching' expression of the VSG using a large genomic repertoire of VSG-encoding genes1-6. Recent studies of antigenic variation in vivo have focused near exclusively on parasites in the bloodstream6-8, but research has shown that many, if not most, parasites reside in the interstitial spaces of tissues9-13. We sought to explore the dynamics of antigenic variation in extravascular parasite populations using VSG-seq7, a high-throughput sequencing approach for profiling VSGs expressed in populations of T. brucei. Here we show that tissues, not the blood, are the primary reservoir of antigenic diversity during both needle- and tsetse bite-initiated T. brucei infections, with more than 75% of VSGs found exclusively within extravascular spaces. We found that this increased diversity is correlated with slower parasite clearance in tissue spaces. Together, these data support a model in which the slower immune response in extravascular spaces provides more time to generate the antigenic diversity needed to maintain a chronic infection. Our findings reveal the important role that extravascular spaces can have in pathogen diversification.

Peptide-coated DNA nanostructures as a platform for control of lysosomal function in cells

DNA nanotechnology is a rapidly growing field that provides exciting tools for biomedical applications. Targeting lysosomal functions with nanomaterials, such as DNA nanostructures (DNs), represents a rational and systematic way to control cell functionality. Here we present a versatile DNA nanostructure-based platform that can modulate a number of cellular functions depending on the concentration and surface decoration of the nanostructure. Utilizing different peptides for surface functionalization of DNs, we were able to rationally modulate lysosomal activity, which in turn translated into the control of cellular function, ranging from changes in cell morphology to modulation of immune signaling and cell death. Low concentrations of decalysine peptide-coated DNs induced lysosomal acidification, altering the metabolic activity of susceptible cells. In contrast, DNs coated with an aurein-bearing peptide promoted lysosomal alkalization, triggering STING activation. High concentrations of decalysine peptide-coated DNs caused lysosomal swelling, loss of cell-cell contacts, and morphological changes without inducing cell death. Conversely, high concentrations of aurein-coated DNs led to lysosomal rupture and mitochondrial damage, resulting in significant cytotoxicity. Our study holds promise for the rational design of a new generation of versatile DNA-based nanoplatforms that can be used in various biomedical applications, like the development of combinatorial anti-cancer platforms, efficient systems for endolysosomal escape, and nanoplatforms modulating lysosomal pH.

Exploring the influence of silicon oxide microchips shape on cellular uptake using imaging flow cytometry

Nano- and micro-carriers of therapeutic molecules offer numerous advantages for drug delivery, and the shape of these particles plays a vital role in their biodistribution and their interaction with cells. However, analysing how microparticles are taken up by cells presents methodological challenges. Qualitative methods like microscopy provide detailed imaging but are time-consuming, whereas quantitative methods such as flow cytometry enable high-throughput analysis but struggle to differentiate between internalised and surface-bound particles. Instead, imaging flow cytometry combines the best of both worlds, offering high-resolution imaging with the efficiency of flow cytometry, allowing for quantitative analysis at the single-cell level. This study focuses on fluorescently labelled silicon oxide microchips of various morphologies but related surface areas and volumes: rectangular cuboids and apex-truncated square pyramid microchips fabricated using photolithography techniques, offering a reliable basis for comparison with the more commonly studied spherical particles. Imaging flow cytometry was utilised to evaluate the effect of particle shape on cellular uptake using RAW 264.7 cells and revealed phagocytosis of particles with all shapes. Increasing the particle dose enhanced the uptake, while macrophage stimulation had minimal effect. Using a ratio particle:cell of 10:1 cuboids and spheres showed an uptake rate of approximately 50%, in terms of the percentage of cells with internalised particles, and the average number of particles taken up per cell ranging from about 1-1.5 particle/cell for all the different shapes. This study indicates how differently shaped micro-carriers offer insights into particle uptake variations, demonstrating the potential of non-spherical micro-carriers for precise drug delivery applications.

Validation of a semi-quantitative scoring system and workflow for analysis of fluorescence quantification in companion animals

Significance

Many commercially available near-infrared (NIR) fluorescence imaging systems lack algorithms for real-time quantifiable fluorescence data. Creation of a workflow for clinical assessment and post hoc analysis may provide clinical researchers with a method for intraoperative fluorescence quantification to improve objective outcome measures.

Aim

Scoring systems and verified image analysis are employed to determine the amount and intensity of fluorescence within surgical specimens both intra and postoperatively.

Approach

Lymph nodes from canine cancer patients were obtained during lymph node extirpation following peritumoral injection of indocyanine green (ICG). First, a semi-quantitative assessment of surface fluorescence was evaluated. Images obtained with a NIR exoscope were analysed to determine fluorescence thresholds and measure fluorescence amount and intensity.

Results

Post hoc fluorescence quantification (threshold of Hue = 165-180, Intensity = 30-255) displayed strong agreement with semi-quantitative scoring (k = 0.9734, p < 0.0001). Fluorescence intensity with either threshold of 35-255 or 45-255 were significant predictors of fluorescence and had high sensitivity and specificity (p < 0.05). Fluorescence intensity and quantification had a strong association (p < 0.001).

Conclusion

The validation of the semi-quantitative scoring system by image analysis provides a method for objective in situ observation of tissue fluorescence. The utilization of thresholding for ICG fluorescence intensity allows post hoc quantification of fluorescence when not built into the imaging system.

A murine model of Trypanosoma brucei-induced myocarditis and cardiac dysfunction

Trypanosoma brucei is a protozoan parasite that causes human and animal African trypanosomiases (HAT and AAT). Cardiac symptoms are commonly reported in HAT patients, and intracardiac parasites with accompanying myocarditis have been observed in both natural hosts and animal models of T. brucei infection. Despite the importance of T. brucei as a cause of cardiac dysfunction and the dramatic socioeconomic impact of African trypanosomiases in sub-Saharan Africa, there are currently no reproducible murine models of T. brucei-associated cardiomyopathy. We present the first clinically relevant, reproducible murine model of cardiac dysfunction in chronic T. brucei infection. Similar to humans, mice showed histological evidence of myocarditis and elevation of serum NT-proBNP with electrocardiographic abnormalities. Serum NT-proBNP levels were elevated prior to the development of severe ventricular dysfunction. On flow cytometry, myocarditis was associated with an increase of most myocardial immune cell populations, including multiple T cell and macrophage subsets, corroborating the notion that T. brucei-associated cardiac damage is an immune-mediated event. This novel mouse model represents a powerful and practical tool to investigate the pathogenesis of T. brucei-mediated heart damage and supports the development of therapeutic options for T. brucei-associated cardiac disease.

DCM-Spheroid Morphs Express PADs and Citrullinated Cytoskeletal Proteins

During investigating the role of peptidylarginine deiminase (PAD) enzymes in dilated cardiomyopathy (DCM), we observed unique spheroid formation in DCM-myofibroblasts that distinguished them from normal cardiac myofibroblasts. The present study aimed to assess the presence of PADs, the extracellular matrix (ECM), and citrullination in DCM spheroids using immunofluorescence staining and imaging techniques. The results revealed that spheroids derived from DCM-myofibroblasts displayed a more distinctive, tightly packed structure compared with those derived from human cardiac fibroblasts. DCM spheroids showed abundant protein expression of the PAD 2, 3, and 4 enzymes. Notably, increased Ki67 protein expression was associated with increased proliferation in DCM spheroids. Cytoskeletal proteins such as Col-1A, vimentin, α-SMA, and F-actin were highly abundant in DCM spheroids. Furthermore, DCM spheroids contained citrullinated cytoskeletal proteins, mainly citrullinated vimentin and citrullinated fibronectin. These observations supported the occurrence of PAD-mediated citrullination of ECM proteins in DCM spheroids. Collectively, these findings describe the distinctive features of DCM spheroids, representing the cellular characteristics of DCM myofibroblasts. Therefore, DCM spheroids can serve as an in vitro model for further investigations of disease morphology and therapeutic efficacy.

Believing is seeing - the deceptive influence of bias in quantitative microscopy

The visual allure of microscopy makes it an intuitively powerful research tool. Intuition, however, can easily obscure or distort the reality of the information contained in an image. Common cognitive biases, combined with institutional pressures that reward positive research results, can quickly skew a microscopy project towards upholding, rather than rigorously challenging, a hypothesis. The impact of these biases on a variety of research topics is well known. What might be less appreciated are the many forms in which bias can permeate a microscopy experiment. Even well-intentioned researchers are susceptible to bias, which must therefore be actively recognized to be mitigated. Importantly, although image quantification has increasingly become an expectation, ostensibly to confront subtle biases, it is not a guarantee against bias and cannot alone shield an experiment from cognitive distortions. Here, we provide illustrative examples of the insidiously pervasive nature of bias in microscopy experiments - from initial experimental design to image acquisition, analysis and data interpretation. We then provide suggestions that can serve as guard rails against bias.

Cell Cycle Mapping Using Multiplexed Immunofluorescence

The development of technologies that allow measurement of the cell cycle at the single-cell level has revealed novel insights into the mechanisms that regulate cell cycle commitment and progression through DNA replication and cell division. These studies have also provided evidence of heterogeneity in cell cycle regulation among individual cells, even within a genetically identical population. Cell cycle mapping combines highly multiplexed imaging with manifold learning to visualize the diversity of "paths" that cells can take through the proliferative cell cycle or into various states of cell cycle arrest. In this chapter, we describe a general protocol of the experimental and computational components of cell cycle mapping. We also provide a comprehensive guide for the design and analysis of experiments, discussing key considerations in detail (e.g., antibody library preparation, analysis strategies, etc.) that may vary depending on the research question being addressed.

Iron oxide nanoparticles trigger endoplasmic reticulum damage in steatotic hepatic cells

Iron oxide nanoparticles (IONPs) are being actively researched in various biomedical applications, particularly as magnetic resonance imaging (MRI) contrast agents for diagnosing various liver pathologies like nonalcoholic fatty liver diseases, nonalcoholic steatohepatitis, and cirrhosis. Emerging evidence suggests that IONPs may exacerbate hepatic steatosis and liver injury in susceptible livers such as those with nonalcoholic fatty liver disease. However, our understanding of how IONPs may affect steatotic cells at the sub-cellular level is still fragmented. Generally, there is a lack of studies identifying the molecular mechanisms of potential toxic and/or adverse effects of IONPs on "non-heathy" in vitro models. In this study, we demonstrate that IONPs, at a dose that does not cause general toxicity in hepatic cells (Alexander and HepG2), induce significant toxicity in steatotic cells (cells loaded with non-toxic doses of palmitic acid). Mechanistically, co-treatment with PA and IONPs resulted in endoplasmic reticulum (ER) stress, accompanied by the release of cathepsin B from lysosomes to the cytosol. The release of cathepsin B, along with ER stress, led to the activation of apoptotic cell death. Our results suggest that it is necessary to consider the interaction between IONPs and the liver, especially in susceptible livers. This study provides important basic knowledge for the future optimization of IONPs as MRI contrast agents for various biomedical applications.

Prevalence and practices of immunofluorescent cell image processing: a systematic review

Background

We performed a systematic review that identified at least 9,000 scientific papers on PubMed that include immunofluorescent images of cells from the central nervous system (CNS). These CNS papers contain tens of thousands of immunofluorescent neural images supporting the findings of over 50,000 associated researchers. While many existing reviews discuss different aspects of immunofluorescent microscopy, such as image acquisition and staining protocols, few papers discuss immunofluorescent imaging from an image-processing perspective. We analyzed the literature to determine the image processing methods that were commonly published alongside the associated CNS cell, microscopy technique, and animal model, and highlight gaps in image processing documentation and reporting in the CNS research field.

Methods

We completed a comprehensive search of PubMed publications using Medical Subject Headings (MeSH) terms and other general search terms for CNS cells and common fluorescent microscopy techniques. Publications were found on PubMed using a combination of column description terms and row description terms. We manually tagged the comma-separated values file (CSV) metadata of each publication with the following categories: animal or cell model, quantified features, threshold techniques, segmentation techniques, and image processing software.

Results

Of the almost 9,000 immunofluorescent imaging papers identified in our search, only 856 explicitly include image processing information. Moreover, hundreds of the 856 papers are missing thresholding, segmentation, and morphological feature details necessary for explainable, unbiased, and reproducible results. In our assessment of the literature, we visualized current image processing practices, compiled the image processing options from the top twelve software programs, and designed a road map to enhance image processing. We determined that thresholding and segmentation methods were often left out of publications and underreported or underutilized for quantifying CNS cell research.

Discussion

Less than 10% of papers with immunofluorescent images include image processing in their methods. A few authors are implementing advanced methods in image analysis to quantify over 40 different CNS cell features, which can provide quantitative insights in CNS cell features that will advance CNS research. However, our review puts forward that image analysis methods will remain limited in rigor and reproducibility without more rigorous and detailed reporting of image processing methods.

Conclusion

Image processing is a critical part of CNS research that must be improved to increase scientific insight, explainability, reproducibility, and rigor.

Sensitivity of endogenous autofluorescence in HeLa cells to the application of external magnetic fields

Dramatically increased levels of electromagnetic radiation in the environment have raised concerns over the potential health hazards of electromagnetic fields. Various biological effects of magnetic fields have been proposed. Despite decades of intensive research, the molecular mechanisms procuring cellular responses remain largely unknown. The current literature is conflicting with regards to evidence that magnetic fields affect functionality directly at the cellular level. Therefore, a search for potential direct cellular effects of magnetic fields represents a cornerstone that may propose an explanation for potential health hazards associated with magnetic fields. It has been proposed that autofluorescence of HeLa cells is magnetic field sensitive, relying on single-cell imaging kinetic measurements. Here, we investigate the magnetic field sensitivity of an endogenous autofluorescence in HeLa cells. Under the experimental conditions used, magnetic field sensitivity of an endogenous autofluorescence was not observed in HeLa cells. We present a number of arguments indicating why this is the case in the analysis of magnetic field effects based on the imaging of cellular autofluorescence decay. Our work indicates that new methods are required to elucidate the effects of magnetic fields at the cellular level.

Tissue-Like 3D Standard and Protocols for Microscope Quality Management

This article outlines a global study conducted by the Association of Biomedical Resource Facilities (ABRF) Light Microscopy Research Group (LMRG). The results present a novel 3D tissue-like biologically relevant standard sample that is affordable and straightforward to prepare. Detailed sample preparation, instrument-specific image acquisition protocols and image analysis methods are presented and made available to the community. The standard consists of sub-resolution and large well characterized relative intensity fluorescence microspheres embedded in a 120 µm thick 3D gel with a refractive index of 1.365. The standard allows the evaluation of several properties as a function of depth. These include the following: 1) microscope resolution with automated analysis of the point-spread function (PSF), 2) automated signal-to-noise ratio analysis, 3) calibration and correction of fluorescence intensity loss, and 4) quantitative relative intensity. Results demonstrate expected refractive index mismatch dependent losses in intensity and resolution with depth, but the relative intensities of different objects at similar depths are maintained. This is a robust standard showing reproducible results across laboratories, microscope manufacturers and objective lens types (e.g., magnification, immersion medium). Thus, these tools will be valuable for the global community to benchmark fluorescence microscopes and will contribute to improved scientific rigor and reproducibility.

Mechanical Regulation of Mitochondrial Dynamics and Function in a 3D-Engineered Liver Tumor Microenvironment

It has become evident that physical stimuli of the cellular microenvironment transmit mechanical cues regulating key cellular functions, such as proliferation, migration, and malignant transformation. Accumulating evidence suggests that tumor cells face variable mechanical stimuli that may induce metabolic rewiring of tumor cells. However, the knowledge of how tumor cells adapt metabolism to external mechanical cues is still limited. We therefore designed soft 3D collagen scaffolds mimicking a pathological mechanical environment to decipher how liver tumor cells would adapt their metabolic activity to physical stimuli of the cellular microenvironment. Here, we report that the soft 3D microenvironment upregulates the glycolysis of HepG2 and Alexander cells. Both cell lines adapt their mitochondrial activity and function under growth in the soft 3D microenvironment. Cells grown in the soft 3D microenvironment exhibit marked mitochondrial depolarization, downregulation of mitochondrially encoded cytochrome c oxidase I, and slow proliferation rate in comparison with stiff monolayer cultures. Our data reveal the coupling of liver tumor glycolysis to mechanical cues. It is proposed here that soft 3D collagen scaffolds can serve as a useful model for future studies of mechanically regulated cellular functions of various liver (potentially other tissues as well) tumor cells.

Virus-free transfection, transient expression, and purification of human cardiac myosin in mammalian muscle cells for biochemical and biophysical assays

Myosin expression and purification is important for mechanistic insights into normal function and mutation induced changes. The latter is particularly important for striated muscle myosin II where mutations cause several debilitating diseases. However, the heavy chain of this myosin is challenging to express and the standard protocol, using C2C12 cells, relies on viral infection. This is time and work intensive and associated with infrastructural demands and biological hazards, limiting widespread use and hampering fast generation of a wide range of mutations. We here develop a virus-free method to overcome these challenges. We use this system to transfect C2C12 cells with the motor domain of the human cardiac myosin heavy chain. After optimizing cell transfection, cultivation and harvesting conditions, we functionally characterized the expressed protein, co-purified with murine essential and regulatory light chains. The gliding velocity (1.5-1.7 µm/s; 25 °C) in the in vitro motility assay as well as maximum actin activated catalytic activity (kcat; 8-9 s-1) and actin concentration for half maximal activity (KATPase; 70-80 µM) were similar to those found previously using virus based infection. The results should allow new types of studies, e.g., screening of a wide range of mutations to be selected for further characterization.

DrSTAR: Tracking real-time nanometer axial changes

Protein interactions with the plasma membrane mediate processes critical for cell viability such as migration and endocytosis, yet our understanding of how recruitment of key proteins correlates with their ability to sense or induce energetically unfavorable plasma membrane shapes remains limited. Simultaneous two-wavelength axial ratiometry (STAR) microscopy provides millisecond time resolution and nanometer axial resolution of protein dynamics at the basal plasma membrane. However, STAR microscopy requires extensive and time-consuming quantitative data processing to access axial (Δz) information. Therefore, addressing questions about the influence of biological and biophysical factors on the interaction between the plasma membrane and protein of interest remains challenging. Here, we overcome the limitations in STAR data processing and present dynamic reference STAR (DrSTAR): a user-friendly, automated, open-source MATLAB-based package. DrSTAR enables processing multiple experimental conditions and biological replicates, employs a novel local background referencing algorithm, and accelerates processing time to facilitate broad adaptation of STAR for studying nanometer axial changes in protein distribution.

Studying T Cell Development in Neonatal and Adult Thymic Slices

T cell development occurs in the thymus and is coordinated temporally and spatially within the highly complex thymic microenvironment. Therefore, T cell selection and maturation events cannot be fully recapitulated using traditional two-dimensional tissue culture in vitro. The thymic slice system provides a highly versatile system for studying T cell development ex vivo while preserving three-dimensional thymic architecture. Using the thymic slice system, T cell selection and maturation events can be visualized by live imaging and quantified by flow cytometry. Here we describe the process for generating slices from neonatal and adult mice.

Practical considerations for quantitative light sheet fluorescence microscopy

Fluorescence microscopy has evolved from a purely observational tool to a platform for quantitative, hypothesis-driven research. As such, the demand for faster and less phototoxic imaging modalities has spurred a rapid growth in light sheet fluorescence microscopy (LSFM). By restricting the excitation to a thin plane, LSFM reduces the overall light dose to a specimen while simultaneously improving image contrast. However, the defining characteristics of light sheet microscopes subsequently warrant unique considerations in their use for quantitative experiments. In this Perspective, we outline many of the pitfalls in LSFM that can compromise analysis and confound interpretation. Moreover, we offer guidance in addressing these caveats when possible. In doing so, we hope to provide a useful resource for life scientists seeking to adopt LSFM to quantitatively address complex biological hypotheses.

Assessment of protein inclusions in cultured cells using automated image analysis

Proteinaceous inclusions are associated with neurodegenerative diseases and cell models are often used to determine genetic and chemical modifiers of their formation. This protocol involves the usage of automated microscopy and machine learning-based image analysis to accurately quantify the levels of protein inclusion formation in cultured cells from fluorescence microscopy images. This protocol is highly scalable and can be applied to a few images or large datasets. For complete details on the use and execution of this protocol, please refer to McAlary et al. (2022).

Quantification of ruffle area and dynamics in live or fixed lung adenocarcinoma cells

Ruffles are actin-rich membrane protrusions implicated in actin reorganization and initiation of cell motility. Here, we describe methods for measuring and analyzing ruffle dynamics in live cells and average ruffle area per cell in fixed samples. The specific steps described are for the analysis of A549 lung adenocarcinoma cells, but the protocol can be applied to other cell types. The protocol has applications for dissecting the signaling events linked to ruffling. For complete details on the use and execution of this protocol, please refer to Cooke et al. (2021).

Quantitative Stimulated Raman Scattering Microscopy: Promises and Pitfalls

Since its first demonstration, stimulated Raman scattering (SRS) microscopy has become a powerful chemical imaging tool that shows promise in numerous biological and biomedical applications. The spectroscopic capability of SRS enables identification and tracking of specific molecules or classes of molecules, often without labeling. SRS microscopy also has the hallmark advantage of signal strength that is directly proportional to molecular concentration, allowing for in situ quantitative analysis of chemical composition of heterogeneous samples with submicron spatial resolution and subminute temporal resolution. However, it is important to recognize that quantification through SRS microscopy requires assumptions regarding both system and sample. Such assumptions are often taken axiomatically, which may lead to erroneous conclusions without proper validation. In this review, we focus on the tacitly accepted, yet complex, quantitative aspect of SRS microscopy. We discuss the various approaches to quantitative analysis, examples of such approaches, challenges in different systems, and potential solutions. Through our examination of published literature, we conclude that a scrupulous approach to experimental design can further expand the powerful and incisive quantitative capabilities of SRS microscopy.

A System to Easily Manage Metadata in Biomedical Research Labs Based on Open-source Software

In most biomedical labs, researchers gather metadata (i.e., all details about the experimental data) in paper notebooks, spreadsheets, or, sometimes, electronic notebooks. When data analyses occur, the related details usually go into other notebooks or spreadsheets, and more metadata are available. The whole thing rapidly becomes very complex and disjointed, and keeping track of all these things can be daunting. Organizing all the relevant data and related metadata for analysis, publication, sharing, or deposit into archives can be time-consuming, difficult, and prone to errors. By having metadata in a centralized system that contains all details from the start, the process is greatly simplified. While lab management software is available, it can be costly and inflexible. The system described here is based on a popular, freely available, and open-source wiki platform. It provides a simple but powerful way for biomedical research labs to set up a metadata management system linking the whole research process. The system enhances efficiency, transparency, reliability, and rigor, which are key factors to improving reproducibility. The flexibility afforded by the system simplifies implementation of specialized lab requirements and future needs. The protocol presented here describes how to create the system from scratch, how to use it for gathering basic metadata, and provides a fully functional version for perusal by the reader. Graphical abstract: Lab Metadata Management System.

When light meets biology - how the specimen affects quantitative microscopy

Fluorescence microscopy images should not be treated as perfect representations of biology. Many factors within the biospecimen itself can drastically affect quantitative microscopy data. Whereas some sample-specific considerations, such as photobleaching and autofluorescence, are more commonly discussed, a holistic discussion of sample-related issues (which includes less-routine topics such as quenching, scattering and biological anisotropy) is required to appropriately guide life scientists through the subtleties inherent to bioimaging. Here, we consider how the interplay between light and a sample can cause common experimental pitfalls and unanticipated errors when drawing biological conclusions. Although some of these discrepancies can be minimized or controlled for, others require more pragmatic considerations when interpreting image data. Ultimately, the power lies in the hands of the experimenter. The goal of this Review is therefore to survey how biological samples can skew quantification and interpretation of microscopy data. Furthermore, we offer a perspective on how to manage many of these potential pitfalls.

Fluorescence Microscopy: A Field Guide for Biologists

Optical microscopy is a tool for observing objects, and features within objects, that are not visible to the unaided eye. In the life sciences, fluorescence microscopy has been widely adopted because it allows us to selectively observe molecules, organelles, and cells at multiple levels of organization. Fluorescence microscopy encompasses numerous techniques and applications that share a specialized technical language and concepts that can create barriers for researchers who are new to this area. Our goal is to meet the needs of researchers new to fluorescence microscopy, by introducing the essential concepts and mindset required to navigate and apply this powerful technology to the laboratory.

Singularity Containers Improve Reproducibility and Ease of Use in Computational Image Analysis Workflows

Reproducing computational workflows in image analysis and microscopy can be a daunting task due to different software versions and dependencies. This is especially true for users with little specific knowledge of scientific computation. To overcome these challenges, we introduce Singularity containers as a useful tool to run and share image analysis workflows among many users, even years later after establishing them. Unfortunately, containers are rarely used so far in the image analysis field. To address this lack of use, we provide a detailed step-by-step protocol to package a state-of-the-art segmentation algorithm into a container on a local Windows machine to run the container on a high-performance cluster computer.

Experimental Designs to Study the Aggregation and Colonization of Biofilms by Video Microscopy With Statistical Confidence

The goal of this study was to quantify the variability of confocal laser scanning microscopy (CLSM) time-lapse images of early colonizing biofilms to aid in the design of future imaging experiments. To accomplish this a large imaging dataset consisting of 16 independent CLSM microscopy experiments was leveraged. These experiments were designed to study interactions between human neutrophils and single cells or aggregates of Staphylococcus aureus (S. aureus) during the initial stages of biofilm formation. Results suggest that in untreated control experiments, variability differed substantially between growth phases (i.e., lag or exponential). When studying the effect of an antimicrobial treatment (in this case, neutrophil challenge), regardless of the inoculation level or of growth phase, variability changed as a frown-shaped function of treatment efficacy (i.e., the reduction in biofilm surface coverage). These findings were used to predict the best experimental designs for future imaging studies of early biofilms by considering differing (i) numbers of independent experiments; (ii) numbers of fields of view (FOV) per experiment; and (iii) frame capture rates per hour. A spreadsheet capable of assessing any user-specified design is included that requires the expected mean log reduction and variance components from user-generated experimental results. The methodology outlined in this study can assist researchers in designing their CLSM studies of antimicrobial treatments with a high level of statistical confidence.

Live-Cell Total Internal Reflection Fluorescence (TIRF) Microscopy to Investigate Protein Internalization Dynamics

The establishment of apicobasal or planar cell polarity involves many events that occur at or near the plasma membrane including focal adhesion dynamics, endocytosis, exocytosis, and cytoskeletal reorganization. It is desirable to visualize these events without interference from other regions deeper within the cell. Total internal reflection fluorescence (TIRF) microscopy utilizes an elegant optical sectioning approach to visualize fluorophores near the sample-coverslip interface. TIRF provides high-contrast fluorescence images with limited background and virtually no out-of-focus light, ideal for visualizing and tracking dynamics near the plasma membrane. In this chapter, we present a general experimental and analysis TIRF pipeline for studying cell surface receptor endocytosis. The approach presented can be easily applied to study other dynamic biological processes at or near the plasma membrane using TIRF microscopy.

ACORBA: Automated workflow to measure Arabidopsis thaliana root tip angle dynamics

The ability of plants to sense and orient their root growth towards gravity is studied in many laboratories. It is known that manual analysis of image data is subjected to human bias. Several semi-automated tools are available for analysing images from flatbed scanners, but there is no solution to automatically measure root bending angle over time for vertical-stage microscopy images. To address these problems, we developed ACORBA, which is an automated software that can measure root bending angle over time from vertical-stage microscope and flatbed scanner images. ACORBA also has a semi-automated mode for camera or stereomicroscope images. It represents a flexible approach based on both traditional image processing and deep machine learning segmentation to measure root angle progression over time. As the software is automated, it limits human interactions and is reproducible. ACORBA will support the plant biologist community by reducing labour and increasing reproducibility of image analysis of root gravitropism.

Characterizing Membrane Traffic in the Early Secretory Pathway Using the RUSH Retention System

The early secretory pathway encompasses the endoplasmic reticulum (ER) and the ER-Golgi intermediate compartment (ERGIC) organelles. The ERGIC is now understood to be a complex cargo sorting hub involved in a variety of cellular and tissue processes, however the traffic pathways to and from the ERGIC are still unclear.Classical methods employed for the analysis of a cargo 's journey along the secretory pathway rely on reversible traffic blocks leading to cargo accumulation in the ER . Although these methods were key to characterize Golgi and post-Golgi traffic routes, their poor specificity to the cargo of interest and limited spatiotemporal resolution make them inadequate for the fine characterization of cargo traffic in the early secretory pathway.In this chapter, we describe a protocol to study the traffic of cargo proteins in the early secretory pathway using the Retention Using Selective Hook (RUSH ) system, a highly specific and sensitive tracking system with a high spatiotemporal resolution. Taking GLUT4 and GLUT1 as examples of unconventionally and conventionally secreted cargo respectively, we describe the steps to clone the cargoes in the RUSH vector and follow and quantify their traffic along the early secretory pathway. This RUSH method can also be used to study the traffic of other cargo proteins in the early secretory pathway.

A Systematic, Open-Science Framework for Quantification of Cell-Types in Mouse Brain Sections Using Fluorescence Microscopy

The ever-expanding availability and evolution of microscopy tools has enabled ground-breaking discoveries in neurobiology, particularly with respect to the analysis of cell-type density and distribution. Widespread implementation of many of the elegant image processing tools available continues to be impeded by the lack of complete workflows that span from experimental design, labeling techniques, and analysis workflows, to statistical methods and data presentation. Additionally, it is important to consider open science principles (e.g., open-source software and tools, user-friendliness, simplicity, and accessibility). In the present methodological article, we provide a compendium of resources and a FIJI-ImageJ-based workflow aimed at improving the quantification of cell density in mouse brain samples using semi-automated open-science-based methods. Our proposed framework spans from principles and best practices of experimental design, histological and immunofluorescence staining, and microscopy imaging to recommendations for statistical analysis and data presentation. To validate our approach, we quantified neuronal density in the mouse barrel cortex using antibodies against pan-neuronal and interneuron markers. This framework is intended to be simple and yet flexible, such that it can be adapted to suit distinct project needs. The guidelines, tips, and proposed methodology outlined here, will support researchers of wide-ranging experience levels and areas of focus in neuroscience research.

Quantifying spatial position in a branched structure in immunostained mouse tissue sections

We have developed a protocol to quantify the position of a cell in a branched structure based on two-dimensional microscopy images of tissue sections. Biological branched structures include organs such as the lungs, kidneys, and pancreas. In these organs, cell fate has been correlated with position, based on a qualitative estimate. However, a quantitative means of evaluating the cell position has been lacking. With this protocol, the correlation between cell fate and cell position was measured in mouse embryonic pancreas. For complete details on the use and execution of this protocol, please refer to Nyeng et al. (2019).

Best practices and tools for reporting reproducible fluorescence microscopy methods

Although fluorescence microscopy is ubiquitous in biomedical research, microscopy methods reporting is inconsistent and perhaps undervalued. We emphasize the importance of appropriate microscopy methods reporting and seek to educate researchers about how microscopy metadata impact data interpretation. We provide comprehensive guidelines and resources to enable accurate reporting for the most common fluorescence light microscopy modalities. We aim to improve microscopy reporting, thus improving the quality, rigor and reproducibility of image-based science.

Modality Agnostic Model for Spatial Resolution in Mass Spectrometry Imaging: Application to MALDI MSI Data

Image resolution in mass spectrometry imaging (MSI) is governed by the sampling probe, the motion of the stage relative to the probe, and the noise inherent for the sample and instrumentation employed. A new image formation model accounting for these variables is presented here. The model shows that the size of the probe, stage velocity, and the rate at which the probe consumes material from the surface govern the amount of blur present in the image. However, the main limiting factor for resolution is the signal-to-noise ratio (SNR). To evaluate blurring and noise effects, a new computational method for measuring lateral resolution in MSI is proposed. A spectral decomposition of the observed image signal and noise is used to determine a resolution number. To evaluate this technique, a silver step edge was prepared. This device was imaged at different pixels sizes using matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI). A modulation transfer function (MTF) and a noise power spectrum (NPS) were computed for each single-ion image, and resolution was defined as the point of intersection between the MTF and the NPS. Finally, the algorithm was also applied to a MALDI MSI tissue data set.

Protein Corona Inhibits Endosomal Escape of Functionalized DNA Nanostructures in Living Cells

DNA nanostructures (DNs) can be designed in a controlled and programmable manner, and these structures are increasingly used in a variety of biomedical applications, such as the delivery of therapeutic agents. When exposed to biological liquids, most nanomaterials become covered by a protein corona, which in turn modulates their cellular uptake and the biological response they elicit. However, the interplay between living cells and designed DNs are still not well established. Namely, there are very limited studies that assess protein corona impact on DN biological activity. Here, we analyzed the uptake of functionalized DNs in three distinct hepatic cell lines. Our analysis indicates that cellular uptake is linearly dependent on the cell size. Further, we show that the protein corona determines the endolysosomal vesicle escape efficiency of DNs coated with an endosome escape peptide. Our study offers an important basis for future optimization of DNs as delivery systems for various biomedical applications.

Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology

Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.

Improved preservation of ovarian tissue morphology that is compatible with antigen detection using a fixative mixture of formalin and acetic acid

STUDY QUESTION

Can ovarian tissue morphology be better preserved whilst enabling histological molecular analyses following fixation with a novel fixative, neutral buffered formalin (NBF) with 5% acetic acid (referred to hereafter as Form-Acetic)?

SUMMARY ANSWER

Fixation with Form-Acetic improved ovarian tissue histology compared to NBF in multiple species while still enabling histological molecular analyses.

WHAT IS KNOWN ALREADY

NBF fixation results in tissue shrinkage in various tissue types including the ovary. Components of ovarian tissue, notably follicles, are particularly susceptible to NBF-induced morphological alterations and can lead to data misrepresentation. Bouin’s solution (which contains 5% acetic acid) better preserves tissue architecture compared to NBF but is limited for immunohistochemical analyses.

STUDY DESIGN, SIZE, DURATION

A comparison of routinely used fixatives, NBF and Bouin’s, and a new fixative, Form-Acetic was carried out. Ovarian tissue was used from three different species: human (n = 5 patients), sheep (n = 3; 6 ovaries; 3 animals per condition) and mouse (n = 14 mice; 3 ovaries from 3 different animals per condition).

PARTICIPANTS/MATERIALS, SETTING, METHODS

Ovarian tissue from humans (aged 13 weeks to 32 years), sheep (reproductively young i.e. 3–6 months) and mice (10 weeks old) were obtained and fixed in 2 ml NBF, Bouin’s or Form-Acetic for 4, 8, and 24 h at room temperature. Tissues were embedded and sectioned. Five-micron sections were stained with haemotoxylin and eosin (H&E) and the percentage of artefact (clear space as a result of shrinkage) between ovarian structures was calculated. Additional histological staining using Periodic acid-Schiff and Masson’s trichrome were performed on 8 and 24 h NBF, Bouin’s and Form-Acetic fixed samples to assess the compatibility of the new fixative with stains. On ovarian tissue fixed for both 8 and 24 h in NBF and Form-Acetic, immunohistochemistry (IHC) studies to detect FOXO3a, FoxL2, collagen IV, laminin and anti-Müllerian hormone (AMH) proteins were performed in addition to the terminal deoxynucleotidyl transferase nick end labelling (TUNEL) assay to determine the compatibility of Form-Acetic fixation with types of histological molecular analyses.

MAIN RESULTS AND THE ROLE OF CHANCE

Fixation in Form-Acetic improved ovarian tissue morphology compared to NBF from all three species and either slightly improved or was comparable to Bouin’s for human, mouse and sheep tissues. Form-Acetic was compatible with H&E, Periodic acid-Schiff and Masson’s trichrome staining and all proteins (FOXO3a, FoxL2, collagen IV and laminin and AMH) could be detected via IHC. Furthermore, Form-Acetic, unlike NBF, enabled antigen recognition for most of the proteins tested without the need for antigen retrieval. Form-Acetic also enabled the detection of damaged DNA via the TUNEL assay using fluorescence.

LARGE SCALE DATA

N/A

LIMITATIONS, REASONS FOR CAUTION

In this study, IHC analysis was performed on a select number of protein types in ovarian tissue thus encouraging further studies to confirm the use of Form-Acetic in enabling the detection of a wider range of protein forms in addition to other tissue types.

WIDER IMPLICATIONS OF THE FINDINGS

The simplicity in preparation of Form-Acetic and its superior preservative properties whilst enabling forms of histological molecular analyses make it a highly valuable tool for studying ovarian tissue. We, therefore, recommend that Form-Acetic replaces currently used fixatives and encourage others to introduce it into their research workflow.

STUDY FUNDING/COMPETING INTEREST(S)

This work was supported by the Oxford Medical Research Council Doctoral Training Programme (Oxford MRC-DTP) grant awarded to B.D.B. (Grant no. MR/N013468/1), the Fondation Hoffmann supporting R.A. and the Petroleum Technology Development Fund (PTDF) awarded to B.V.A.

Confocal and TIRF microscopy based approaches to visualize arrestin trafficking in living cells

Arrestins are key proteins that serve as versatile scaffolds to control and mediate G protein coupled receptors (GPCR) activity. Arrestin control of GPCR functions involves their recruitment from the cytosol to plasma membrane-localized GPCRs and to endosomal compartments, where they mediate internalization, sorting and signaling of GPCRs. Several methods can be used to monitor trafficking of arrestins; however, live fluorescence imaging remains the method of choice to both assess arrestin recruitment to ligand-activated receptors and to monitor its dynamic subcellular localization. Here, we present two approaches based on Total Internal Fluorescence (TIRF) microscopy and confocal microscopy to visualize arrestin trafficking in live cells in real time and to assess their co-localization with the GPCR of interest and their localization at specific subcellular locations.

A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis?

Considerable attention has been recently paid to improving replicability and reproducibility in life science research. This has resulted in commendable efforts to standardize a variety of reagents, assays, cell lines and other resources. However, given that microscopy is a dominant tool for biologists, comparatively little discussion has been offered regarding how the proper reporting and documentation of microscopy relevant details should be handled. Image processing is a critical step of almost any microscopy-based experiment; however, improper, or incomplete reporting of its use in the literature is pervasive. The chosen details of an image processing workflow can dramatically determine the outcome of subsequent analyses, and indeed, the overall conclusions of a study. This Review aims to illustrate how proper reporting of image processing methodology improves scientific reproducibility and strengthens the biological conclusions derived from the results.

A guide to accurate reporting in digital image acquisition - can anyone replicate your microscopy data?

Recent technological advances have made microscopy indispensable in life science research. Its ubiquitous use, in turn, underscores the importance of ensuring that microscopy-based experiments are replicable and that the resulting data comparable. While there has been a wealth of review articles, practical guides and conferences devoted to the topic of maintaining standard instrument operating conditions, the paucity of attention dedicated to properly documenting microscopy experiments is undeniable. This lack of emphasis on accurate reporting extends beyond life science researchers themselves, to the review panels and editorial boards of many journals. Such oversight at the final step of communicating a scientific discovery can unfortunately negate the many valiant efforts made to ensure experimental quality control in the name of scientific reproducibility. This Review aims to enumerate the various parameters that should be reported in an imaging experiment by illustrating how their inconsistent application can lead to irreconcilable results.

4D Widefield Fluorescence Imaging of Appressorium Morphogenesis by Magnaporthe oryzae

Fluorescence microscopy has become a widely used and indispensable tool for the M. oryzae research community, providing unique insight into appressorium formation and function. A common practice within the field is to acquire and present images of a number of different conidia, expressing a fluorescent fusion protein of interest, at various stages of infectious development, therein providing a representative "snapshot" of the population at a given point in time. Furthermore, these images typically show only a single focal plane through the specimen (2D) and therefore lack, often valuable, volumetric information. While this approach has its advantages, the continuous imaging of (multiple) single conidia in three dimensions (3D), and over time (4D), can provide additional insight into the spatial and temporal dynamics of fluorescent fusion proteins, and the subcellular structures and compartments they label, in living cells. Here we describe our typical workflow for the 4D live-cell imaging of appressorium morphogenesis in vitro using two-color widefield fluorescence microscopy and briefly outline some important considerations for strain construction, and downstream image processing and visualization.

Menoci: lightweight extensible web portal enhancing data management for biomedical research projects

BACKGROUND

Biomedical research projects deal with data management requirements from multiple sources like funding agencies' guidelines, publisher policies, discipline best practices, and their own users' needs. We describe functional and quality requirements based on many years of experience implementing data management for the CRC 1002 and CRC 1190. A fully equipped data management software should improve documentation of experiments and materials, enable data storage and sharing according to the FAIR Guiding Principles while maximizing usability, information security, as well as software sustainability and reusability.

RESULTS

We introduce the modular web portal software menoci for data collection, experiment documentation, data publication, sharing, and preservation in biomedical research projects. Menoci modules are based on the Drupal content management system which enables lightweight deployment and setup, and creates the possibility to combine research data management with a customisable project home page or collaboration platform.

CONCLUSIONS

Management of research data and digital research artefacts is transforming from individual researcher or groups best practices towards project- or organisation-wide service infrastructures. To enable and support this structural transformation process, a vital ecosystem of open source software tools is needed. Menoci is a contribution to this ecosystem of research data management tools that is specifically designed to support biomedical research projects.

Hepatic Tumor Cell Morphology Plasticity under Physical Constraints in 3D Cultures Driven by YAP-mTOR Axis

Recent studies undoubtedly show that the mammalian target of rapamycin (mTOR) and the Hippo–Yes-associated protein 1 (YAP) pathways are important mediators of mechanical cues. The crosstalk between these pathways as well as de-regulation of their signaling has been implicated in multiple tumor types, including liver tumors. Additionally, physical cues from 3D microenvironments have been identified to alter gene expression and differentiation of different cell lineages. However, it remains incompletely understood how physical constraints originated in 3D cultures affect cell plasticity and what the key mediators are of such process. In this work, we use collagen scaffolds as a model of a soft 3D microenvironment to alter cellular size and study the mechanotransduction that regulates that process. We show that the YAP-mTOR axis is a downstream effector of 3D cellular culture-driven mechanotransduction. Indeed, we found that cell mechanics, dictated by the physical constraints of 3D collagen scaffolds, profoundly affect cellular proliferation in a YAP–mTOR-mediated manner. Functionally, the YAP–mTOR connection is key to mediate cell plasticity in hepatic tumor cell lines. These findings expand the role of YAP–mTOR-driven mechanotransduction to the control hepatic tumor cellular responses under physical constraints in 3D cultures. We suggest a tentative mechanism, which coordinates signaling rewiring with cytoplasmic restructuring during cell growth in 3D microenvironments.

Hypothesis-driven quantitative fluorescence microscopy - the importance of reverse-thinking in experimental design

One of the challenges in modern fluorescence microscopy is to reconcile the conventional utilization of microscopes as exploratory instruments with their emerging and rapidly expanding role as a quantitative tools. The contribution of microscopy to observational biology will remain enormous owing to the improvements in acquisition speed, imaging depth, resolution and biocompatibility of modern imaging instruments. However, the use of fluorescence microscopy to facilitate the quantitative measurements necessary to challenge hypotheses is a relatively recent concept, made possible by advanced optics, functional imaging probes and rapidly increasing computational power. We argue here that to fully leverage the rapidly evolving application of microscopes in hypothesis-driven biology, we not only need to ensure that images are acquired quantitatively but must also re-evaluate how microscopy-based experiments are designed. In this Opinion, we present a reverse logic that guides the design of quantitative fluorescence microscopy experiments. This unique approach starts from identifying the results that would quantitatively inform the hypothesis and map the process backward to microscope selection. This ensures that the quantitative aspects of testing the hypothesis remain the central focus of the entire experimental design.

Quantitative assessment of morphology and sub-cellular changes in macrophages and trophoblasts during inflammation

In pregnancy during an inflammatory condition, macrophages present at the feto-maternal junction release an increased amount of nitric oxide (NO) and pro-inflammatory cytokines such as TNF-α and INF-γ, which can disturb the trophoblast functions and pregnancy outcome. Measurement of the cellular and sub-cellular morphological modifications associated with inflammatory responses are important in order to quantify the extent of trophoblast dysfunction for clinical implication. With this motivation, we investigated morphological, cellular and sub-cellular changes in externally inflamed RAW264.7 (macrophage) and HTR-8/SVneo (trophoblast) using structured illumination microscopy (SIM) and quantitative phase microscopy (QPM). We monitored the production of NO, changes in cell membrane and mitochondrial structure of macrophages and trophoblasts when exposed to different concentrations of pro-inflammatory agents (LPS and TNF-α). In vitro NO production by LPS-induced macrophages increased 22-fold as compared to controls, whereas no significant NO production was seen after the TNF-α challenge. Under similar conditions as with macrophages, trophoblasts did not produce NO following either LPS or the TNF-α challenge. Super-resolution SIM imaging showed changes in the morphology of mitochondria and the plasma membrane in macrophages following the LPS challenge and in trophoblasts following the TNF-α challenge. Label-free QPM showed a decrease in the optical thickness of the LPS-challenged macrophages while TNF-α having no effect. The vice-versa is observed for the trophoblasts. We further exploited machine learning approaches on a QPM dataset to detect and to classify the inflammation with an accuracy of 99.9% for LPS-challenged macrophages and 98.3% for TNF-α-challenged trophoblasts. We believe that the multi-modal advanced microscopy methodologies coupled with machine learning approach could be a potential way for early detection of inflammation.

Fundamentals of Microscopy

The light (or optical) microscope is the icon of science. The aphorism "seeing is believing" is often quoted in scientific papers involving microscopy. Unlike many scientific instruments, the light microscope will deliver an image however badly it is set up. Fluorescence microscopy is a widely used research tool across all disciplines of biological and biomedical science. Most universities and research institutions have microscopes, including confocal microscopes. This introductory paper in a series detailing advanced light microscopy techniques explains the foundations of both electron and light microscopy for biologists and life scientists working with the mouse. An explanation is given of how an image is formed. A description is given of how to set up a light microscope, whether it be a brightfield light microscope on the laboratory bench, a widefield fluorescence microscope, or a confocal microscope. These explanations are accompanied by operational protocols. A full explanation on how to set up and adjust a microscope according to the principles of Köhler illumination is given. The importance of Nyquist sampling is discussed. Guidelines are given on how to choose the best microscope to image the particular sample or slide preparation that you are working with. These are the basic principles of microscopy that a researcher must have an understanding of when operating core bioimaging facility instruments, in order to collect high-quality images. © 2020 The Authors. Basic Protocol 1: Setting up Köhler illumination for a brightfield microscope Basic Protocol 2: Aligning the fluorescence bulb and setting up Köhler illumination for a widefield fluorescence microscope Basic Protocol 3: Generic protocol for operating a confocal microscope.

Customizable live-cell imaging chambers for multimodal and multiplex fluorescence microscopy

Using multiple imaging modalities while performing independent experiments in parallel can greatly enhance the throughput of microscopy-based research, but requires the provision of appropriate experimental conditions in a format that meets the optical requirements of the microscope. Although customized imaging chambers can meet these challenges, the difficulty of manufacturing custom chambers and the relatively high cost and design inflexibility of commercial chambers has limited the adoption of this approach. Herein, we demonstrate the use of 3D printing to produce inexpensive, customized, live-cell imaging chambers that are compatible with a range of imaging modalities, including super-resolution microscopy. In this approach, biocompatible plastics are used to print imaging chambers designed to meet the specific needs of an experiment, followed by adhesion of the printed chamber to a glass coverslip, producing a chamber that is impermeant to liquids and that supports the growth and imaging of cells over multiple days. This approach can also be used to produce moulds for casting microfluidic devices made of polydimethylsiloxane. The utility of these chambers is demonstrated using designs for multiplex microscopy, imaging under shear, chemotaxis, and general cellular imaging. Together, this approach represents an inexpensive yet highly customizable approach for producing imaging chambers that are compatible with modern microscopy techniques.

Iron Oxide Nanoparticle-Induced Autophagic Flux Is Regulated by Interplay between p53-mTOR Axis and Bcl-2 Signaling in Hepatic Cells

Iron oxide-based nanoparticles have been repeatedly shown to affect lysosomal-mediated signaling. Recently, nanoparticles have demonstrated an ability to modulate autophagic flux via lysosome-dependent signaling. However, the precise underlying mechanisms of such modulation as well as the impact of cellular genetic background remain enigmatic. In this study, we investigated how lysosomal-mediated signaling is affected by iron oxide nanoparticle uptake in three distinct hepatic cell lines. We found that nanoparticle-induced lysosomal dysfunction alters sub-cellular localization of pmTOR and p53 proteins. Our data indicate that alterations in the sub-cellular localization of p53 protein induced by nanoparticle greatly affect the autophagic flux. We found that cells with high levels of Bcl-2 are insensitive to autophagy initiated by nanoparticles. Altogether, our data identify lysosomes as a central hub that control nanoparticle-mediated responses in hepatic cells. Our results provide an important fundamental background for the future development of targeted nanoparticle-based therapies.