Standard Fluorescence Microscopy Research Articles

Validation of an Organ Mapping Antibody Panel for Cyclical Immunofluorescence Microscopy on Normal Human Kidneys.

The lack of standardization in antibody validation remains a major contributor to irreproducibility of human research. To address this, we have applied a standardized approach to validate a panel antibodies to identify 18 major cell types and 5 extracellular matrix compartments in the human kidney by immunofluorescence (IF) microscopy. We have used these to generate an organ mapping antibody panel for 2-D and 3-D Cyclical Immunofluorescence (CyCIF) to provide a more detailed method to evaluate of tissue segmentation and volumes using a larger panel of markers than would normally be possible using standard fluorescence microscopy. CyCIF also makes it possible to perform multiplexed IF microscopy of whole slide images, which is a distinct advantage over other multiplexed imaging technologies that are applicable to limited fields of view. This enables a broader view of cell distributions across larger anatomical regions, allowing a better chance to capture localized regions of dysfunction in diseased tissues. These methods are broadly accessible to any laboratory with a fluorescence microscope, enabling spatial cellular phenotyping in normal and disease states. We also provide a detailed solution for image alignment between CyCIF cycles that can be used by investigators to perform these studies without programming experience using open-sourced software. This ability to perform multiplexed imaging without specialized instrumentation or computational skills, opens the door to integration with more highly dimensional molecular imaging modalities such as spatial transcriptomics and imaging mass spectrometry, enabling the discovery of molecular markers of specific cell types and how these are altered in disease.

Fluorescent tools for the standardized work in Gram-negative bacteria

Standardized and thoroughly characterized genetic tools are a prerequisite for studying cellular processes to ensure the reusability and consistency of experimental results. The discovery of fluorescent proteins (FPs) represents a milestone in the development of genetic reporters for monitoring transcription or protein localization in vivo. FPs have revolutionized our understanding of cellular dynamics by enabling the real-time visualization and tracking of biological processes. Despite these advancements, challenges remain in the appropriate use of FPs, specifically regarding their proper application, protein turnover dynamics, and the undesired disruption of cellular functions. Here, we systematically compared a comprehensive set of 15 FPs and assessed their performance in vivo by focusing on key parameters, such as signal over background ratios and protein stability rates, using the Gram-negative model organism Salmonella enterica as a representative host. We evaluated four protein degradation tags in both plasmid- and genome-based systems and our findings highlight the necessity of introducing degradation tags to analyze time-sensitive cellular processes. We demonstrate that the gain of dynamics mediated by the addition of degradation tags impacts the cell-to-cell heterogeneity of plasmid-based but not genome-based reporters. Finally, we probe the applicability of FPs for protein localization studies in living cells using standard and super-resolution fluorescence microscopy. In summary, our study underscores the importance of careful FP selection and paves the way for the development of improved genetic reporters to enhance the reproducibility and reliability of fluorescence-based research in Gram-negative bacteria and beyond.

A novel imaging method (FIM-ID) reveals that myofibrillogenesis plays a major role in the mechanically induced growth of skeletal muscle

An increase in mechanical loading, such as that which occurs during resistance exercise, induces radial growth of muscle fibers (i.e. an increase in cross-sectional area). Muscle fibers are largely composed of myofibrils, but whether radial growth is mediated by an increase in the size of the myofibrils (i.e. myofibril hypertrophy) and/or the number of myofibrils (i.e. myofibrillogenesis) is not known. Electron microscopy (EM) can provide images with the level of resolution that is needed to address this question, but the acquisition and subsequent analysis of EM images is a time- and cost-intensive process. To overcome this, we developed a novel method for visualizing myofibrils with a standard fluorescence microscope (fluorescence imaging of myofibrils with image deconvolution [FIM-ID]). Images from FIM-ID have a high degree of resolution and contrast, and these properties enabled us to develop pipelines for automated measurements of myofibril size and number. After extensively validating the automated measurements, we used both mouse and human models of increased mechanical loading to discover that the radial growth of muscle fibers is largely mediated by myofibrillogenesis. Collectively, the outcomes of this study offer insight into a fundamentally important topic in the field of muscle growth and provide future investigators with a time- and cost-effective means to study it.

A novel imaging method (FIM-ID) reveals that myofibrillogenesis plays a major role in the mechanically induced growth of skeletal muscle.

An increase in mechanical loading, such as that which occurs during resistance exercise, induces radial growth of muscle fibers (i.e. an increase in cross-sectional area). Muscle fibers are largely composed of myofibrils, but whether radial growth is mediated by an increase in the size of the myofibrils (i.e. myofibril hypertrophy) and/or the number of myofibrils (i.e. myofibrillogenesis) is not known. Electron microscopy (EM) can provide images with the level of resolution that is needed to address this question, but the acquisition and subsequent analysis of EM images is a time- and cost-intensive process. To overcome this, we developed a novel method for visualizing myofibrils with a standard fluorescence microscope (fluorescence imaging of myofibrils with image deconvolution [FIM-ID]). Images from FIM-ID have a high degree of resolution and contrast, and these properties enabled us to develop pipelines for automated measurements of myofibril size and number. After extensively validating the automated measurements, we used both mouse and human models of increased mechanical loading to discover that the radial growth of muscle fibers is largely mediated by myofibrillogenesis. Collectively, the outcomes of this study offer insight into a fundamentally important topic in the field of muscle growth and provide future investigators with a time- and cost-effective means to study it.

3D Amplified Single-Cell RNA and Protein Imaging Identifies Oncogenic Transcript Subtypes in B-Cell Acute Lymphoblastic Leukemia.

Simultaneous in situ detection of transcript and protein markers at the single-cell level is essential for gaining a better understanding of tumor heterogeneity and for predicting and monitoring treatment responses. However, the limited accessibility to advanced 3D imaging techniques has hindered their rapid implementation. Here, we present a 3D single-cell imaging technique, termed 3D digital rolling circle amplification (4DRCA), capable of the multiplexed and amplified simultaneous digital quantification of single-cell RNAs and proteins using standard fluorescence microscopy and off-the-shelf reagents. We generated spectrally distinguishable DNA amplicons from molecular markers through an integrative protocol combining single-cell RNA and protein assays and directly enumerated the amplicons by leveraging an open-source algorithm for 3D deconvolution with a custom-built automatic gating algorithm. With 4DRCA, we were able to simultaneously quantify surface protein markers and cytokine transcripts in T-lymphocytes. We also show that 4DRCA can distinguish BCR-ABL1 fusion transcript positive B-cell acute lymphoblastic leukemia cells with or without CD19 protein expression. The accessibility and extensibility of 4DRCA render it broadly applicable to other cell-based diagnostic workflows, enabling sensitive and accurate single-cell RNA and protein profiling.

I spy: Factors influencing the observation of oxytetracycline in calcified structures of fishes viewed using standard light and fluorescence microscopy.

The antibiotic oxytetracycline (OTC) is a fluorochrome marker, and fluorescence microscopy is used to view OTC marks in fishes' calcified structures. However, OTC marks have been observed in calcified structures using standard light microscopy for multiple species. Therefore, we conducted an experiment to investigate potential factors (i.e., season, total length of fish, growth rate, and sex) influencing the observation of OTC in calcified structures (otoliths and fin rays or spines) from channel catfish Ictalurus punctatus, gray redhorse Moxostoma congestum, Guadalupe bass Mircopterus treculii, and redbreast sunfish Lepomis auritus viewed using standard light and fluorescence microscopy. OTC stains were not observed in any otoliths under standard light; however, OTC marks were commonly observed in I. punctatus spines using standard light microscopy (56.2%). Ninety-nine percent of otoliths and 88.9% of spines and fin rays had a visible fluorescent OTC mark when viewed using fluorescence microscopy. There was a negative relationship between the observed OTC mark and total length of fish for each season, but fish injected in the summer had the most structures with an observed OTC mark under either light condition. Understanding how OTC marking is affected by biological processes and environmental conditions will assist in future studies that rely on chemical marking of calcified structures by increasing efficacy of OTC marking and interpretation of marks.

Expansion microscopy for visualization of protein clusters in cultured cells and brain tissues

Expansion microscopy for visualization of protein clusters in cultured cells and brain tissues

Organelle-specific phase contrast microscopy (OS-PCM) enables facile correlation study of organelles and proteins.

Current methods for studying organelle and protein interactions and correlations depend on multiplex fluorescent labeling, which is experimentally complex and harmful to cells. Here we propose to solve this challenge via OS-PCM, where organelles are imaged and segmented without labels, and combined with standard fluorescence microscopy of protein distributions. In this work, we develop new neural networks to obtain unlabeled organelle, nucleus and membrane predictions from a single 2D image. Automated analysis is also implemented to obtain quantitative information regarding the spatial distribution and co-localization of both protein and organelle, as well as their relationship to the landmark structures of nucleus and membrane. Using mitochondria and DRP1 protein as a proof-of-concept, we conducted a correlation study where only DRP1 is labeled, with results consistent with prior reports utilizing multiplex labeling. Thus our work demonstrates that OS-PCM simplifies the correlation study of organelles and proteins.

Ontogenesis of the Mouse Ocular Surface Lymphatic Vascular Network.

Ocular lymphatic vessels play major physiological role in eye homeostasis and their dysfunction can contribute to the progression of several eye diseases. In this study, we characterized their spatiotemporal development and the cellular mechanisms occurring during their ontogenesis in the mouse eye. Whole mount immunofluorescent staining and imaging by standard or lightsheet fluorescence microscopy were performed on late embryonic and early postnatal eye mouse samples. We observed that the ocular surface lymphatic vascular network develops at the early postnatal stages (between P0 and P5) from two nascent trunks arising at the nasal side on both sides of the nictitating membrane. These nascent vessels further branch and encircle the whole eye surface by sprouting lymphangiogenesis. In addition, we got evidence for the existence of a transient lymphvasculogenesis process generating lymphatic vessel fragments that will mostly formed the corneolimbal lymphatic vasculature which further connect to the conjunctival lymphatic network. Our results also support that CD206-positive macrophages can transdifferentiate and then integrate into the lymphatic neovessels. Several complementary cellular processes participate in the development of the lymphatic ocular surface vasculature. This knowledge paves the way for the design of new therapeutic strategies to interfere with ocular lymphatic vessel formation when needed.

Deep-qGFP: A Generalist Deep Learning Assisted Pipeline for Accurate Quantification of Green Fluorescent Protein Labeled Biological Samples in Microreactors.

Absolute quantification of biological samples provides precise numerical expression levels, enhancing accuracy, and performance for rare templates. Current methodologies, however, face challenges-flow cytometers are costly and complex, whereas fluorescence imaging, relying on software or manual counting, is time-consuming and error-prone. It is presented that Deep-qGFP, a deep learning-aided pipeline for the automated detection and classification of green fluorescent protein (GFP) labeled microreactors, enables real-time absolute quantification. This approach achieves an accuracy of 96.23% and accurately measures the sizes and occupancy status of microreactors using standard laboratory fluorescence microscopes, providing precise template concentrations. Deep-qGFP demonstrates remarkable speed, quantifying over 2000 microreactors across ten images in just 2.5seconds, with a dynamic range of 56.52-1569.43copiesµL-1 . The method demonstrates impressive generalization capabilities, successfully applied to various GFP-labeling scenarios, including droplet-based, microwell-based, and agarose-based applications. Notably, Deep-qGFP is the first all-in-one image analysis algorithm successfully implemented in droplet digital polymerase chain reaction (PCR), microwell digital PCR, droplet single-cell sequencing, agarose digital PCR, and bacterial quantification, without requiring transfer learning, modifications, or retraining. This makes Deep-qGFP readily applicable in biomedical laboratories and holds potential for broader clinical applications.

Machine learning-based morphological quantification of replicative senescence in human fibroblasts.

Although aging has been investigated extensively at the organismal and cellular level, the morphological changes that individual cells undergo along their replicative lifespan have not been precisely quantified. Here, we present the results of a readily accessible machine learning-based pipeline that uses standard fluorescence microscope and open access software to quantify the minute morphological changes that human fibroblasts undergo during their replicative lifespan in culture. Applying this pipeline in a widely used fibroblast cell line (IMR-90), we find that advanced replicative age robustly increases (+28-79%) cell surface area, perimeter, number and total length of pseudopodia, and nuclear surface area, while decreasing cell circularity, with phenotypic changes largely occurring as replicative senescence is reached. These senescence-related morphological changes are recapitulated, albeit to a variable extent, in primary dermal fibroblasts derived from human donors of different ancestry, age, and sex groups. By performing integrative analysis of single-cell morphology, our pipeline further classifies senescent-like cells and quantifies how their numbers increase with replicative senescence in IMR-90 cells and in dermal fibroblasts across all tested donors. These findings provide quantitative insights into replicative senescence, while demonstrating applicability of a readily accessible computational pipeline for high-throughput cell phenotyping in aging research.

Assessing aptamer-analyte binding kinetics by microfluidic fluorescence microscopy

Kinetic measurement plays a crucial role in understanding aptamer binding mechanisms and identifying appropriate aptamers for clinical and research applications. Current techniques, while well established, generally require large sample volumes, bulky and expensive instruments operated by trained personnel, and are hence not readily accessible to resource-limited research laboratories. This paper presents a fluorescence microscopy-based microfluidic assay for measuring aptamer-analyte binding kinetics in a simple and cost-effective manner. Kinetic measurements are achieved by monitoring time-course fluorescence of fluorescently labeled aptamers as they bind to the targets trapped in a microfluidic chip. Fluorescence measurements are performed on a standard fluorescence microscope and are accessible to laboratories with only modest resources. Moreover, microfluidic technology allows efficient and cost-effective immobilization of small amounts of target molecules or live cells as well as flow-based manipulation of aptamers for the measurements. Kinetic measurements of aptamer binding to immunoglobulin E protein and CCRF-CEM cells have yielded results consistent with those obtained from established methods, demonstrating the potential utility of our method for exploring aptamer-target interactions and identifying aptamers that best suit specific given biomedical applications.

Optimising multiplex immunofluorescence staining for characterising the tumour immune micro-environment.

Exploring the tumour microenvironment provides insight into the unique interaction between the host and tumour. Ultimately, its study improves understanding of how an individual mounts and achieves an anti-tumour immune response. In the context of colorectal cancer, immune biomarkers within the tumour microenvironment outperform traditional histopathological staging in predicting disease recurrence. Multiplex immunofluorescence enables simultaneous assessment of multiple markers to provide a highly accurate classification of immune cells and their spatial characterisation relative to tumour tissue. Further, automated slide staining provides staining consistency and reduces labour costs. Image acquisition using a non-spectral scanner allows more researchers to utilise multiplexed immunofluorescence for translational research. Herein we describe the optimisation process of conducting automated staining using a five-colour, tyramide signal amplification-based multiplex immunofluorescence panel. Using antibodies against CD3, CD8, CD103 and cytokeratin, the panel characterises T cell populations within human colorectal adenocarcinoma tissue. We provide an overview of primary antibody titration and the development of tyramide signal amplification immunofluorescence monoplex assays. We detail the processes of antibody stripping and the role of exogenous horseradish peroxidase inhibition to facilitate multiplexing. An account of determining the staining sequence and fluorophore assignment is provided. We describe image acquisition using a standard fluorescence microscope slide scanner and the management of spectral crosstalk using this system. Finally, we briefly document the digital image analysis required to characterise cells and determine their spatial distribution within the colorectal tumour microenvironment.

Trifunctional Linkers Enable Improved Visualization of Actin by Expansion Microscopy.

Expansion microscopy (ExM) revolutionized the field of super-resolution microscopy by allowing for subdiffraction resolution fluorescence imaging on standard fluorescence microscopes. However, it has been found that it is hard to visualize actin filaments efficiently using ExM. To improve actin imaging, multifunctional molecules have been designed with moderate success. Here, we present optimized methods for phalloidin conjugate grafting that have a high efficiency for both cellular and tissue samples. Our optimized strategy improves anchoring and signal retention by ∼10 times. We demonstrate the potential of optimized trifunctional linkers (TRITON) for actin imaging in combination with immunolabeling using different ExM protocols. 10X ExM of actin labeled with optimized TRITON enabled us to visualize the periodicity of actin rings in cultured hippocampal neurons and brain slices by Airyscan confocal microscopy. Thus, TRITON linkers provide an efficient grafting method, especially in cases in which the concentration of target-bound monomers is insufficient for high-quality ExM.

B-110 Validation of Digital and Automated anti-dsDNA IFA Interpretations Using the dIFine Automated Fluorescent Microscope System

Abstract Background Detection of anti-double stranded DNA antibodies (anti-dsDNA) by the indirect fluorescent antibody (IFA) assay is a well-established tool for aiding in the diagnosis of systemic lupus erythematosus (SLE). ZEUS Scientific has manufactured an FDA-cleared anti-dsDNA IFA test system for decades, which relies upon manual interpretation of qualitative results using a standard fluorescent microscope. This same anti-dsDNA IFA test system was recently utilized to train software, in conjunction with a specialized fluorescent microscope (collectively termed dIFine), towards automating qualitative result interpretation. The objective of this study was to validate the reproducibility, sensitivity, and specificity of the ZEUS anti-dsDNA IFA test system, in conjunction with the dIFine automated microscope. Methods Multi-site reproducibility study–2 low-positive, 2 mid-positive, 2 high-positive, and 2 negative serum samples were assembled to create a reproducibility panel. The sample identities of the panel members were scrambled prior to testing. The panel was assayed via the ZEUS anti-dsDNA-IFA test system at a 1:10 screening dilution, in triplicate, twice per day, on five days, at three different laboratories (including ZEUS Scientific). At each laboratory, the processed slides were interpreted manually by two operators, then scanned by dIFine to generate digital images of the wells, as well as an automated qualitative result interpretation. The digital images of each slide well were also interpreted by two operators, resulting in 3 independent interpretations per sample, for each operator and instrument (Manual, Digital, Automated). The number of slide wells processed for interpretation at each laboratory was: 8 samples × 30 replicates each = 240 total. Clinical study–300 serum samples derived from donors previously diagnosed with SLE were assembled. A control cohort consisting of 360 samples from donors previously diagnosed with other rheumatic and non-rheumatic diseases was also assembled. The sample identities were scrambled for both cohorts prior to testing. The 660 samples were assayed at a 1:10 screening dilution using the ZEUS anti-dsDNA IFA test system at ZEUS Scientific. Manual, digital, and automated interpretations were carried out at ZEUS Scientific as described above. Results Reproducibility (Actual/Expected): [Site 1 - Operator A - Manual (240/240), Digital (240/240); Site 1 - Operator B - Manual (240/240), Digital (240/240); Site 1 - Automated - (231/240)]. [Site 2 - Operator A - Manual (240/240), Digital (240/240); [Site 2 - Operator B - Manual (240/240), Digital (240/240); Site 2 - Automated - (236/240)]. [Site 3 - Operator A - Manual (240/240), Digital (238/240); Site 3 - Operator B - Manual (240/240), Digital (238/240); Site 3 - Automated - (231/240)]. Sensitivity for SLE cohort (Positive/Total, %): [Operator A - Manual, (79/300, 26.3%), Digital (79/300, 26.3%)]; [Operator B - Manual, (79/300, 26.3%), Digital (79/300, 26.3%), Automated (81/300, 27.0%)]. Specificity for control cohort (Negative/Total): [Operator A - Manual, (358/360, 99.4%), Digital (358/360, 99.4%)]; [Operator B - Manual, (358/360, 99.4%), Digital (358/360, 99.4%), Automated (358/360, 99.4%)]. Conclusions These validation studies demonstrate that the ZEUS anti-dsDNA-IFA test system, in conjunction with the automated dIFine microscope, yields highly reproducible and accurate results derived from digital and automated interpretations.

Morphological and lipid metabolism alterations in macrophages exposed to model environmental nanoplastics traced by high-resolution synchrotron techniques.

The release of nanoplastics (NPs) in the environment is a significant health concern for long-term exposed humans. Although their usage has certainly revolutionized several application fields, at nanometer size, NPs can easily interact at the cellular level, resulting in potential harmful effects. Micro/Nanoplastics (M/NPs) have a demonstrated impact on mammalian endocrine components, such as the thyroid, adrenal gland, testes, and ovaries, while more investigations on prenatal and postnatal exposure are urgently required. The number of literature studies on the NPs' presence in biological samples is increasing. However, only a few offer a close study on the model environmental NP-immune system interaction exploited by advanced microscopy techniques. The present study highlights substantial morphological and lipid metabolism alterations in human M1 macrophages exposed to labeled polypropylene and polyvinyl chloride nanoparticles (PP and PVC NPs) (20 μg/ml). The results are interpreted by advanced microscopy techniques combined with standard laboratory tests and fluorescence microscopy. We report the accurate detection of polymeric nanoparticles doped with cadmium selenide quantum dots (CdSe-QDs NPs) by following the Se (L line) X-ray fluorescence emission peak at higher sub-cellular resolution, compared to the supportive light fluorescence microscopy. In addition, scanning transmission X-ray microscopy (STXM) imaging successfully revealed morphological changes in NP-exposed macrophages, providing input for Fourier transform infrared (FTIR) spectroscopy analyses, which underlined the chemical modifications in macromolecular components, specifically in lipid response. The present evidence was confirmed by quantifying the lipid droplet (LD) contents in PP and PVC NPs-exposed macrophages (0-100 μg/ml) by Oil Red O staining. Hence, even at experimental NPs' concentrations and incubation time, they do not significantly affect cell viability; they cause an evident lipid metabolism impairment, a hallmark of phagocytosis and oxidative stress.

Correlative Imaging of Three-Dimensional Cell Culture on Opaque Bioscaffolds for Tissue Engineering Applications.

Three-dimensional (3D) tissue engineering (TE) is a prospective treatment that can be used to restore or replace damaged musculoskeletal tissues, such as articular cartilage. However, current challenges in TE include identifying materials that are biocompatible and have properties that closely match the mechanical properties and cellular microenvironment of the target tissue. Visualization and analysis of potential 3D porous scaffolds as well as the associated cell growth and proliferation characteristics present additional problems. This is particularly challenging for opaque scaffolds using standard optical imaging techniques. Here, we use graphene foam (GF) as a 3D porous biocompatible substrate, which is scalable, reproducible, and a suitable environment for ATDC5 cell growth and chondrogenic differentiation. ATDC5 cells are cultured, maintained, and stained with a combination of fluorophores and gold nanoparticles to enable correlative microscopic characterization techniques, which elucidate the effect of GF properties on cell behavior in a 3D environment. Most importantly, the staining protocol allows for direct imaging of cell growth and proliferation on opaque scaffolds using X-ray MicroCT, including imaging growth of cells within the hollow GF branches, which is not possible with standard fluorescence and electron microscopy techniques.

Multiplexed Barcoding Image Analysis for Immunoprofiling and Spatial Mapping Characterization in the Single-Cell Analysis of Paraffin Tissue Samples

Multiplexed imaging technology using antibody barcoding with oligonucleotides, which sequentially detects multiple epitopes in the same tissue section, is an effective methodology for tumor evaluation that improves the understanding of the tumor microenvironment. The visualization of protein expression in formalin-fixed, paraffin-embeddedtissues is achieved when a specific fluorophore is annealed to an antibody-bound barcode via complementary oligonucleotides and then sample imaging is performed; indeed, this method allows for the use of customizable panels of more than 40 antibodies in a single tissue staining reaction. This method is compatible with fresh frozen tissue, formalin-fixed, paraffin-embedded tissue, cultured cells, and peripheral blood mononuclear cells, meaning that researchers can use this technology to view a variety of sample types at single-cell resolution. This method starts with a manual staining and fixing protocol, and all the antibody barcodes are applied using an antibody cocktail. The staining fluidics instrument is fully automated and performs iterative cycles of labeling, imaging, and removing spectrally distinct fluorophores until all the biomarkers have been imaged using a standard fluorescence microscope. The images are then collected and compiled across all the imaging cycles to achieve single-cell resolution for all the markers. The single-step staining and gentle fluorophore removal not only allow for highly multiplexed biomarker analysis but also preserve the sample for additional downstream analysis if desired (e.g., hematoxylin and eosin staining). Furthermore, the image analysis software enables image processing-drift compensation, background subtraction, cell segmentation, and clustering-as well as the visualization and analysis of the images and cell phenotypes for the generation of spatial network maps. In summary, this technology employs a computerized microfluidics system and fluorescence microscope to iteratively hybridize, image, and strip fluorescently labeled DNA probes that are complementary to tissue-bound, oligonucleotide-conjugated antibodies.

LEMONADE: Lego-like membrane tension analyzer based on self-assembled DNA elastic networks.

Membrane tension regulates and is affected by many cellular processes, including cell motility and membrane trafficking. However, the role of membrane tension in such processes is poorly understood because of difficulties in measuring dynamic membrane tension changes in live cells. Current approaches for membrane tension measurements can be broadly divided into two categories. In the first, fluorescence-based signals from small molecular probes that insert into cellular membranes are used. These allow convenient mapping of the signals throughout the cell membrane, but probe local membrane properties which are not always easy to relate to membrane tension. In addition, they are prone to artefacts due to membrane heterogenicities. The second type of approach relies on pulling a thin membrane tether from the cell surface. The restoring force acting on the tether is related to membrane tension and can be measured using optical tweezers. However, this approach requires specialized equipment and tension is measured at a single location. To overcome these challenges, we are developing a novel approach based on the self-assembly of an elastic network on the cell surface we call LEMONADE (Lego-like membrane tensionanalyzer based on self-assembled DNA elastic networks). The new membrane tension sensor relies on membrane-anchored Lego-like DNA nanostructures that are linked by elastic connectors with a FRET pair modification. Cell membrane area changes will result in transient FRET signals which can be detected throughout the cell surface using standard live fluorescence microscopy. We will report our progress in the design, assembly, and calibration of LEMONADE.

Extended DNA Fibers for High-Resolution Mapping.

DNA fiber-FISH is an easy and simple light microscopic method to map unique and repeat sequences relative to each other at the molecular scale. A standard fluorescence microscope and a DNA labeling kit are sufficient to visualize DNA sequences from any tissue or organ. Despite the enormous progress of high-throughput sequencing technologies, DNA fiber-FISH remains a unique and indispensable tool to detect chromosomal rearrangements and to demonstrate differences between related species at high resolution. We discuss standard and alternative steps to easily prepare extended DNA fibers for high-resolution FISH mapping.