A solid beta-sheet structure is formed at the surface of FUS droplets during aging.

Phase transitions are important to understand cell dynamics, and the maturation of liquid droplets is relevant to neurodegenerative disorders. We combined NMR and Raman spectroscopies with microscopy to follow, over a period of days to months, droplet maturation of the protein fused in sarcoma (FUS). Our study reveals that the surface of the droplets plays a critical role in this process, while RNA binding prevents it. The maturation kinetics are faster in an agarose-stabilized biphasic sample compared with a monophasic condensed sample, owing to the larger surface-to-volume ratio. In addition, Raman spectroscopy reports structural differences upon maturation between the inside and the surface of droplets, which is comprised of ß-sheet content, as revealed by solid-state NMR. In agreement with these observations, a solid crust-like shell is observed at the surface using microaspiration. Ultimately, matured droplets were converted into fibrils involving the prion-like domain as well as the first RGG motif.

Structural control of fibrin bioactivity by mechanical deformation.

Fibrin is the fibrous protein network that comprises blood clots; it is uniquely capable of bearing very large tensile strains (up to 200%) due to multiscale force accommodation mechanisms. Fibrin is also a biochemical scaffold for numerous enzymes and blood factors. The biomechanics and biochemistry of fibrin have been independently studied. However, comparatively little is known about how fibrin biomechanics and biochemistry are coupled: how does fibrin deformation influence its biochemistry? In this study, we show that mechanically induced protein structural changes in fibrin affect fibrin biochemistry. We find that tensile deformation of fibrin leads to molecular structural transitions of α-helices to ß-sheets, which reduced binding of tissue plasminogen activator (tPA), an enzyme that initiates fibrin lysis. Moreover, binding of tPA and Thioflavin T, a commonly used ß-sheet marker, were mutually exclusive, further demonstrating the mechano-chemical control of fibrin biochemistry. Finally, we demonstrate that structural changes in fibrin suppressed the biological activity of platelets on mechanically strained fibrin due to reduced αIIbß3 integrin binding. Our work shows that mechanical strain regulates fibrin molecular structure and biological activity in an elegant mechano-chemical feedback loop, which possibly extends to other fibrous biopolymers.

Lipid droplets as substrates for protein phase separation.

Membrane-associated protein phase separation plays critical roles in cell biology, driving essential cellular phenomena from immune signaling to membrane traffic. Importantly, by reducing dimensionality from three to two dimensions, lipid bilayers can nucleate phase separation at far lower concentrations compared with those required for phase separation in solution. How might other intracellular lipid substrates, such as lipid droplets, contribute to nucleation of phase separation? Distinct from bilayer membranes, lipid droplets consist of a phospholipid monolayer surrounding a core of neutral lipids, and they are energy storage organelles that protect cells from lipotoxicity and oxidative stress. Here, we show that intrinsically disordered proteins can undergo phase separation on the surface of synthetic and cell-derived lipid droplets. Specifically, we find that the model disordered domains FUS LC and LAF-1 RGG separate into protein-rich and protein-depleted phases on the surfaces of lipid droplets. Owing to the hydrophobic nature of interactions between FUS LC proteins, increasing ionic strength drives an increase in its phase separation on droplet surfaces. The opposite is true for LAF-1 RGG, owing to the electrostatic nature of its interprotein interactions. In both cases, protein-rich phases on the surfaces of synthetic and cell-derived lipid droplets demonstrate molecular mobility indicative of a liquid-like state. Our results show that lipid droplets can nucleate protein condensates, suggesting that protein phase separation could be key in organizing biological processes involving lipid droplets.

Intrinsic Burst-Blinking Nanographenes for Super-Resolution Bioimaging.

Single-molecule localization microscopy (SMLM) is a powerful technique to achieve super-resolution imaging beyond the diffraction limit. Although various types of blinking fluorophores are currently considered for SMLM, intrinsic blinking fluorophores remain rare at the single-molecule level. Here, we report the synthesis of nanographene-based intrinsic burst-blinking fluorophores for highly versatile SMLM. We image amyloid fibrils in air and in various pH solutions without any additive and lysosome dynamics in live mammalian cells under physiological conditions. In addition, the single-molecule labeling of nascent proteins in primary sensory neurons was achieved with azide-functionalized nanographenes via click chemistry. SMLM imaging reveals higher local translation at axonal branching with unprecedented detail, while the size of translation foci remained similar throughout the entire network. These various results demonstrate the potential of nanographene-based fluorophores to drastically expand the applicability of super-resolution imaging.

Assessing the impact of extracellular matrix fiber orientation on breast cancer cellular metabolism.

The extracellular matrix (ECM) is a dynamic and complex microenvironment that modulates cell behavior and cell fate. Changes in ECM composition and architecture have been correlated with development, differentiation, and disease progression in various pathologies, including breast cancer [1]. Studies have shown that aligned fibers drive a pro-metastatic microenvironment, promoting the transformation of mammary epithelial cells into invasive ductal carcinoma via the epithelial-to-mesenchymal transition (EMT) [2]. The impact of ECM orientation on breast cancer metabolism, however, is largely unknown. Here, we employ two non-invasive imaging techniques, fluorescence-lifetime imaging microscopy (FLIM) and intensity-based multiphoton microscopy, to assess the metabolic states of cancer cells cultured on ECM-mimicking nanofibers in a random and aligned orientation. By tracking the changes in the intrinsic fluorescence of nicotinamide adenine dinucleotide and flavin adenine dinucleotide, as well as expression levels of metastatic markers, we reveal how ECM fiber orientation alters cancer metabolism and EMT progression. Our study indicates that aligned cellular microenvironments play a key role in promoting metastatic phenotypes of breast cancer as evidenced by a more glycolytic metabolic signature on nanofiber scaffolds of aligned orientation compared to scaffolds of random orientation. This finding is particularly relevant for subsets of breast cancer marked by high levels of collagen remodeling (e.g. pregnancy associated breast cancer), and may serve as a platform for predicting clinical outcomes within these subsets [3-6].

Comparing lipid remodeling of brown adipose tissue, white adipose tissue, and liver after one-week high fat diet intervention with quantitative Raman microscopy.

Brown adipose tissue (BAT) consists of highly metabolically active adipocytes that catabolize nutrients to produce heat. Playing an active role in triacylglycerol (TAG) clearance, research has shown that dietary fatty acids can modulate the TAG chemistry deposition in BAT after weeks-long dietary intervention, similar to what has been shown in white adipose tissue (WAT). Our objective was to compare the influence of sustained, nonchronic dietary intervention (a 1-week interval) on WAT and interscapular BAT lipid metabolism and deposition in situ. We use quantitative, label-free chemical microscopy to show that 1 week of high fat diet (HFD) intervention results in dramatically larger lipid droplet (LD) growth in BAT (and liver) compared to LD growth in inguinal WAT (IWAT). Moreover, BAT showed lipid remodeling as increased unsaturated TAGs in LDs, resembling the dietary lipid composition, while WAT (and liver) did not show lipid remodeling on this time scale. Concurrently, expression of genes involved in lipid metabolism, particularly desaturases, was reduced in BAT and liver from HFD-fed mice after 1 week. Our data show that BAT lipid chemistry remodels exceptionally fast to dietary lipid intervention compared WAT, which further points towards a role in TAG clearance.

Role of Solvent Compatibility in the Phase Behavior of Binary Solutions of Weakly Associating Multivalent Polymers.

Condensate formation of biopolymer solutions, prominently those of various intrinsically disordered proteins (IDPs), is often driven by "sticky" interactions between associating residues, multivalently present along the polymer backbone. Using a ternary mean-field "stickers-and-spacers" model, we demonstrate that if sticker association is of the order of a few times the thermal energy, a delicate balance between specific binding and nonspecific polymer-solvent interactions gives rise to a particularly rich ternary phase behavior under physiological circumstances. For a generic system represented by a solution comprising multiassociative scaffold and client polymers, the difference in solvent compatibility between the polymers modulates the nature of isothermal liquid-liquid phase separation (LLPS) between associative and segregative. The calculations reveal regimes of dualistic phase behavior, where both types of LLPS occur within the same phase diagram, either associated with the presence of multiple miscibility gaps or a flip in the slope of the tie-lines belonging to a single coexistence region.

Correlated interfacial water transport and proton conductivity in perfluorosulfonic acid membranes.

Water must be effectively transported and is also essential for maximizing proton conductivity within fuel-cell proton-exchange membranes (PEMs). Therefore, identifying relationships between PEM properties, water transport, and proton conductivity is essential for designing optimal PEMs. Here, we use coherent Raman spectroscopy to quantify real-time, in situ diffusivities of water subspecies, bulk-like and nonbulk-like (interfacial) water, in five different perfluorosulfonic acid (PFSA) PEMs. Although the PEMs were chemically diverse, water transport within them followed the same rule: Total water diffusivity could be represented by a linear combination of the bulk-like and interfacial water diffusivities. Moreover, the diffusivity of interfacial water was consistently larger than that of bulk-like water. These measurements of microscopic transport were combined with through-plane proton conductivity measurements to reveal the correlation between interfacial water transport and proton conductivity. Our results demonstrate the importance of maximizing the diffusivity and fractional contribution of interfacial water to maximize the proton conductivity in PFSA PEMs.

EVICAN-a balanced dataset for algorithm development in cell and nucleus segmentation.

MOTIVATION: Deep learning use for quantitative image analysis is exponentially increasing. However, training accurate, widely deployable deep learning algorithms requires a plethora of annotated (ground truth) data. Image collections must contain not only thousands of images to provide sufficient example objects (i.e. cells), but also contain an adequate degree of image heterogeneity. RESULTS: We present a new dataset, EVICAN-Expert visual cell annotation, comprising partially annotated grayscale images of 30 different cell lines from multiple microscopes, contrast mechanisms and magnifications that is readily usable as training data for computer vision applications. With 4600 images and ∼26 000 segmented cells, our collection offers an unparalleled heterogeneous training dataset for cell biology deep learning application development. AVAILABILITY AND IMPLEMENTATION: The dataset is freely available (https://edmond.mpdl.mpg.de/imeji/collection/l45s16atmi6Aa4sI?q=). Using a Mask R-CNN implementation, we demonstrate automated segmentation of cells and nuclei from brightfield images with a mean average precision of 61.6 % at a Jaccard Index above 0.5.

Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force.

Small solutes have been shown to alter the lateral organization of cell membranes and reconstituted phospholipid bilayers; however, the mechanisms by which these changes happen are still largely unknown. Traditionally, both experiment and simulation studies have been restricted to testing only a few compounds at a time, failing to identify general molecular descriptors or chemical properties that would allow extrapolating beyond the subset of considered solutes. In this work, we probe the competing energetics of inserting a solute in different membrane environments by means of the potential of mean force. We show that these calculations can be used as a computationally efficient proxy to establish whether a solute will stabilize or destabilize domain phase separation. Combined with umbrella-sampling simulations and coarse-grained molecular dynamics simulations, we are able to screen solutes across a wide range of chemistries and polarities. Our results indicate that for the system under consideration, preferential partitioning and therefore effectiveness in altering membrane phase separation are strictly linked to the location of insertion in the bilayer (i.e., midplane or interface). Our approach represents a fast and simple tool for obtaining structural and thermodynamic insight into the partitioning of small molecules between lipid domains and its relation to phase separation, ultimately providing a platform for identifying the key determinants of this process.

Label-free CARS microscopy reveals similar triacylglycerol acyl chain length and saturation in myocellular lipid droplets of athletes and individuals with type 2 diabetes.

AIMS/HYPOTHESIS: Intramyocellular lipid (IMCL) content associates with development of insulin resistance, albeit not in insulin-sensitive endurance-trained athletes (trained). Qualitative and spatial differences in muscle lipid composition may underlie this so-called athlete's paradox. Here we studied triacylglycerol (TAG) composition of individual myocellular lipid droplets (LDs) in trained individuals and individuals with type 2 diabetes mellitus. METHODS: Trained ([Formula: see text] 71.0 ± 1.6 ml O2 [kg lean body mass (LBM)]-1 min-1), normoglycaemic (fasting glucose 5.1 ± 0.1 mmol/l) individuals and untrained ([Formula: see text] 36.8 ± 1.5 ml O2 [kg LBM]-1 min-1) individuals with type 2 diabetes (fasting glucose 7.4 ± 0.5 mmol/l), with similar IMCL content (3.5 ± 0.7% vs 2.5 ± 0.3%, p = 0.241), but at opposite ends of the insulin sensitivity spectrum (glucose infusion rate 93.8 ± 6.6 vs 25.7 ± 5.3 µmol [kg LBM]-1 min-1 for trained individuals and those with type 2 diabetes, respectively) were included from our database in the present study. We applied in situ label-free broadband coherent anti-Stokes Raman scattering (CARS) microscopy to sections from skeletal muscle biopsies to measure TAG acyl chain length and saturation of myocellular LDs. This approach uniquely permits examination of individual LDs in their native environment, in a fibre-type-specific manner, taking into account LD size and subcellular location. RESULTS: Despite a significant difference in insulin sensitivity, we observed remarkably similar acyl chain length and saturation in trained and type 2 diabetic individuals (chain length: 18.12 ± 0.61 vs 18.36 ± 0.43 number of carbons; saturation: 0.37 ± 0.05 vs 0.38 ± 0.06 number of C=C bonds). Longer acyl chains or higher saturation (lower C=C number) could be detected in subpopulations of LDs, i.e. large LDs (chain length: 18.11 ± 0.48 vs 18.63 ± 0.57 carbon number) and subsarcolemmal LDs (saturation: 0.34 ± 0.02 vs 0.36 ± 0.04 C=C number), which are more abundant in individuals with type 2 diabetes. CONCLUSIONS/INTERPRETATION: In contrast to reports of profound differences in the lipid composition of lipids extracted from skeletal muscle from trained and type 2 diabetic individuals, our in situ, LD-specific approach detected only modest differences in TAG composition in LD subpopulations, which were dependent on LD size and subcellular location. If, and to what extent, these modest differences can impact insulin sensitivity remains to be elucidated. Graphical abstract.

Nonlinear, dissipative phenomena in whole blood clot mechanics.

When a thrombus breaks off and embolizes it can occlude vital vessels such as those of the heart, lung, or brain. These thromboembolic conditions are responsible for 1 in 4 deaths worldwide. Thrombus resistance to embolization is driven by its intrinsic fracture toughness as well as other, non-surface-creating dissipative mechanisms. In our current work, we identify and quantify these latter mechanisms toward future studies that aim to delineate fracture from other forms of dissipation. To this end, we use an in vitro thrombus mimic system to produce whole blood clots and explore their dissipative mechanics under simple uniaxial extension, cyclic loading, and stress-relaxation. We found that whole blood clots exhibit Mullins-like effect, hysteresis, permanent set, strain-rate dependence, and nonlinear stress-relaxation. Interestingly, we found that performing these tests under dry or submerged conditions did not change our results. However, performing these tests under room temperature or body temperature conditions yielded differences. Importantly, because we use venous blood our work is most closely related to venous in vivo blood clots. Overall, we have demonstrated that whole blood clots show several dissipative phenomena - similarly to hydrogels - that will be critical to our understanding of thrombus embolization.

Nanoparticle amount, and not size, determines chain alignment and nonlinear hardening in polymer nanocomposites.

Polymer nanocomposites-materials in which a polymer matrix is blended with nanoparticles (or fillers)-strengthen under sufficiently large strains. Such strain hardening is critical to their function, especially for materials that bear large cyclic loads such as car tires or bearing sealants. Although the reinforcement (i.e., the increase in the linear elasticity) by the addition of filler particles is phenomenologically understood, considerably less is known about strain hardening (the nonlinear elasticity). Here, we elucidate the molecular origin of strain hardening using uniaxial tensile loading, microspectroscopy of polymer chain alignment, and theory. The strain-hardening behavior and chain alignment are found to depend on the volume fraction, but not on the size of nanofillers. This contrasts with reinforcement, which depends on both volume fraction and size of nanofillers, potentially allowing linear and nonlinear elasticity of nanocomposites to be tuned independently.

Nanographenes: Ultrastable, Switchable, and Bright Probes for Super-Resolution Microscopy.

Super-resolution fluorescence microscopy has enabled important breakthroughs in biology and materials science. Implementations such as single-molecule localization microscopy (SMLM) and minimal emission fluxes (MINFLUX) microscopy in the localization mode exploit fluorophores that blink, i.e., switch on and off, stochastically. Here, we introduce nanographenes, namely large polycyclic aromatic hydrocarbons that can also be regarded as atomically precise graphene quantum dots, as a new class of fluorophores for super-resolution fluorescence microscopy. Nanographenes exhibit outstanding photophysical properties: intrinsic blinking even in air, excellent fluorescence recovery, and stability over several months. As a proof of concept for super-resolution applications, we use nanographenes in SMLM to generate 3D super-resolution images of silica nanocracks. Our findings open the door for the widespread application of nanographenes in super-resolution fluorescence microscopy.

Quantitative Mapping of Triacylglycerol Chain Length and Saturation Using Broadband CARS Microscopy.

Lipid droplets (LDs), present in many cell types, are highly dynamic organelles that store neutral lipids, primarily triacylglycerols (TAGs). With the discovery of new LD functions (e.g., in immune response, protein clearage, and occurrence with disease), new methods to study LD chemical composition in situ are necessary. We present an approach for in situ, quantitative TAG analysis using label-free, coherent Raman microscopy that allows deciphering LD TAG composition in different biochemically complex samples with submicrometer spatial resolution. Employing a set of standard TAGs, we generate a spectral training matrix capturing the variation caused in Raman-like spectra by TAG backbone, chain length, and number of double bonds per chain, as well as the presence of proteins or other diluting molecules. Comparing our fitting approach to gas chromatography measurements for mixtures of standard TAGs and food oils, we find the root mean-square error for the prediction of TAG chemistry to be 0.69 CH2 and 0.15 #C=C. When progressing to more complex samples such as oil emulsions and LDs in various eukaryotic cells, we find good agreement with bulk gas chromatography measurements. For differentiated adipocytes, we find a significant increase in the number of double bonds in small LDs (below 2 µm in diameter) compared to large LDs (above 2 µm in diameter). Coupled with a relatively limited sample preparation requirement, this approach should enable rapid and accurate TAG LD analysis for a variety of cell biology and technological applications.

Automated cell segmentation in FIJI® using the DRAQ5 nuclear dye.

BACKGROUND: Image segmentation and quantification are essential steps in quantitative cellular analysis. In this work, we present a fast, customizable, and unsupervised cell segmentation method that is based solely on Fiji (is just ImageJ)®, one of the most commonly used open-source software packages for microscopy analysis. In our method, the "leaky" fluorescence from the DNA stain DRAQ5 is used for automated nucleus detection and 2D cell segmentation. RESULTS: Based on an evaluation with HeLa cells compared to human counting, our algorithm reached accuracy levels above 92% and sensitivity levels of 94%. 86% of the evaluated cells were segmented correctly, and the average intersection over union score of detected segmentation frames to manually segmented cells was above 0.83. Using this approach, we quantified changes in the projected cell area, circularity, and aspect ratio of THP-1 cells differentiating from monocytes to macrophages, observing significant cell growth and a transition from circular to elongated form. In a second application, we quantified changes in the projected cell area of CHO cells upon lowering the incubation temperature, a common stimulus to increase protein production in biotechnology applications, and found a stark decrease in cell area. CONCLUSIONS: Our method is straightforward and easily applicable using our staining protocol. We believe this method will help other non-image processing specialists use microscopy for quantitative image analysis.

Double stimuli-responsive polysaccharide block copolymers as green macrosurfactants for near-infrared photodynamic therapy.

The NIR absorbing photosensitizer phthalocyanine zinc (PC(Zn)) was stabilized in aqueous media as water-dispersible nanoparticles with a reduction- and pH-responsive full polysaccharide block copolymer. A cellular uptake and also photo switchable intracellular activity of the cargo upon irradiation at wavelengths in the near infrared region were shown. The block copolymer was synthesized by applying a copper-free click strategy based on a thiol exchange reaction, creating an amphiphilic double-stimuli-responsive mixed disulfide. The dual-sensitive polysaccharide micelles represent a non-toxic and biodegradable green macrosurfactant for the delivery of phthalocyanine zinc. By encapsulation into micellar nanoparticles, the bioavailability of PC(Zn) increased significantly, enabling smart photodynamic therapy for future applications in cancer-related diseases.

Characterizing the hydrophobic-to-hydrophilic transition of electrolyte structuring in proton exchange membrane mimicking surfaces.

The surface density of charged sulfonic acid head groups in a perfluorosulfonic acid (PFSA) proton exchange membrane determines the hydrophilicity of the ionic channels and is thus critical for the structuring and transport of water and protons. The mechanism through which the head group density affects the structuring of water and ions is unknown, largely due to experimental challenges in systematically varying the density in an appropriate model system resembling the ionic channels. Here, we present a model system for PFSA membrane ionic channels using self-assembled monolayers with a tunable surface density of sulfonic acid and methyl groups to tune surface hydrophilicity. Atomic force microscopy force-distance measurements were used to quantify the hydration forces and deduce the interfacial electrolyte structure. The measured force profiles indicate a pronounced change of the electrolyte layering density at the surface with an unexpectedly sharp hydrophobic-to-hydrophilic transition when the surface shows a contact angle of ∼37°. Using an extended Derjaguin-Landau-Verwey-Overbeek model including the Hydra force, we quantify diffuse double layer charges and characteristic hydration lengths as a function of sulfonic acid group density on the surface. Translating our results to PFSA membranes, these findings have two implications: (1) the density of sulfonic acid head groups can have a dramatic effect on the local solvent structuring of water inside the ionic channels and (2) they support a view where two types of water (solution) exist in PFSA ionic channels - a structured (shell/surface) and a non-structured (bulk) water. This offers an interesting perspective on how different head group densities lead to changes in water and proton transport and macroscopic membrane conductivity properties based on hydration layer characteristics.

Superresolution imaging reveals structurally distinct periodic patterns of chromatin along pachytene chromosomes.

During meiosis, homologous chromosomes associate to form the synaptonemal complex (SC), a structure essential for fertility. Information about the epigenetic features of chromatin within this structure at the level of superresolution microscopy is largely lacking. We combined single-molecule localization microscopy (SMLM) with quantitative analytical methods to describe the epigenetic landscape of meiotic chromosomes at the pachytene stage in mouse oocytes. DNA is found to be nonrandomly distributed along the length of the SC in condensed clusters. Periodic clusters of repressive chromatin [trimethylation of histone H3 at lysine (Lys) 27 (H3K27me3)] are found at 500-nm intervals along the SC, whereas one of the ends of the SC displays a large and dense cluster of centromeric histone mark [trimethylation of histone H3 at Lys 9 (H3K9me3)]. Chromatin associated with active transcription [trimethylation of histone H3 at Lys 4 (H3K4me3)] is arranged in a radial hair-like loop pattern emerging laterally from the SC. These loops seem to be punctuated with small clusters of H3K4me3 with an average spread larger than their periodicity. Our findings indicate that the nanoscale structure of the pachytene chromosomes is constrained by periodic patterns of chromatin marks, whose function in recombination and higher order genome organization is yet to be elucidated.

Measuring Intracellular Secondary Structure of a Cell-Penetrating Peptide in Situ.

Cell-penetrating peptides (CPPs) are short peptide sequences that can translocate across cellular plasma membranes and are thus potential delivery vectors for diagnostic and therapeutic applications. Many CPPs exhibit some sort of structural polymorphism, where the secondary structure of the peptide is altered strongly by its local environment, which is believed to facilitate membrane translocation and uptake. However, much less is known about the fate and structure of CPPs within cells largely due to measurement difficulty. Here we employ isotopic labeling combined with hyperspectral, quantitative coherent Raman microscopy to localize a model CPP-penetratin-and determine its secondary structure in different cellular compartments. Our results show that penetratin is mostly α-helical in the cytosol and acquires a more ß-sheet and random coil character in the nucleus. The increased helicity in the cytosol is similar to that seen in previous studies with model lipid membranes, suggesting that the peptide is associated with membranes in, e.g., endosomes (or lysosomes) in the cytosol. The ability to both localize and determine the secondary structure of a CPP within cells is critical for clarifying the mechanism of peptide-mediated translocation and delivery of cargo molecules to specific cellular destinations.