Rate-Engineered Plasmon-Enhanced Fluorescence for Real-Time Microsecond Dynamics of Single Biomolecules.

Single-molecule fluorescence has revealed a wealth of biochemical processes but does not give access to submillisecond dynamics involved in transient interactions and molecular dynamics. Here we overcome this bottleneck and demonstrate record-high photon count rates of >107 photons/s from single plasmon-enhanced fluorophores. This is achieved by combining two conceptual novelties: first, we balance the excitation and decay rate enhancements by the antenna's volume, resulting in maximum fluorescence intensity. Second, we enhance the triplet decay rate using a multicomponent surface chemistry that minimizes microsecond blinking. We demonstrate applications to two exemplary molecular processes: we first reveal transient encounters and hybridization of DNA with a 1 µs temporal resolution. Second, we exploit the field gradient around the nanoparticle as a molecular ruler to reveal microsecond intramolecular dynamics of multivalent complexes. Our results pave the way toward real-time microsecond studies of biochemical processes using an implementation compatible with existing single-molecule fluorescence methods.

Characterization of DNA-protein complexes by nanoparticle tracking analysis and their association with systemic lupus erythematosus.

Nanotechnology enables investigations of single biomacromolecules, but technical challenges have limited the application in liquid biopsies, for example, blood plasma. Nonetheless, tools to characterize single molecular species in such samples represent a significant unmet need with the increasing appreciation of the physiological importance of protein structural changes at nanometer scale. Mannose-binding lectin (MBL) is an oligomeric plasma protein and part of the innate immune system through its ability to activate complement. MBL also serves a role as a scavenger for cellular debris, especially DNA. This may link functions of MBL with several inflammatory diseases in which cell-free DNA now appears to play a role, but mechanistic insight has been lacking. By making nanoparticle tracking analysis possible in human plasma, we now show that superoligomeric structures of MBL form nanoparticles with DNA. These oligomers correlate with disease activity in systemic lupus erythematosus patients. With the direct quantification of the hydrodynamic radius, calculations following the principles of Taylor dispersion in the blood stream connect the size of these complexes to endothelial inflammation, which is among the most important morbidities in lupus. Mechanistic insight from an animal model of lupus supported that DNA-stabilized superoligomers stimulate the formation of germinal center B cells and drive loss of immunological tolerance. The formation involves an inverse relationship between the concentration of MBL superoligomers and antibodies to double-stranded DNA. Our approach implicates the structure of DNA-protein nanoparticulates in the pathobiology of autoimmune diseases.

Advanced bioengineering of female germ cells to preserve fertility.

Oogenesis and folliculogenesis are considered as complex and species-specific cellular differentiation processes, which depend on the in vivo ovarian follicular environment and endocrine cues. Considerable efforts have been devoted to driving the differentiation of female primordial germ cells toward mature oocytes outside of the body. The recent experimental attempts have laid stress on offering a suitable microenvironment to assist the in vitro folliculogenesis and oogenesis. Despite developing a variety of bioengineering techniques and generating functional mature gametes through in vitro oogenesis in earlier studies, we still lack knowledge of appropriate microenvironment conditions for building biomimetic culture systems for female fertility preservation. Therefore, this review paper can provide a source for a large body of scientists developing cutting-edge in vitro culture systems for female germ cells or setting up the next generation of reproductive medicine as feasible options for female infertility treatment. The focal point of this review outlines advanced bioengineering technologies such as 3D biofabricated hydrogels/scaffolds and microfluidic systems utilized with female germlines for fertility preservation through in vitro folliculogenesis and oogenesis.

Nanoparticle Adsorption on Antifouling Polymer Brushes.

Polymer brushes have been widely used to functionalize surfaces and provide antifouling capabilities against proteins and cells. Many efforts have focused on methods for functionalization of antifouling polymer brush surfaces for interactions with specific cells, proteins, and bacteria, but none have focused on immobilizing nanoparticles (NPs) on these surfaces. This article demonstrates that both pristine NPs and protein-coated NPs can adsorb onto well-functioning antifouling polymer brush coatings formed from poly-l-lysine-graft-poly(ethylene glycol) (PLL-g-PEG) and methoxy PEG-thiol. The role of ionic strength in solution, substrate surface material, and NP surface charge in the interaction was investigated to explore the forces behind the interaction. The adsorption of different types of NPs onto the surface was studied, determining that polystyrene, gold, carbon black, and silica particles can adsorb onto PLL-g-PEG. We show that the approach can be applied in, and studied by, both surface plasmon resonance and fluorescence imaging and suggest its application as a means to study NP-protein interactions, such as the protein corona. NPs self-assembled at antifouling polymer brush surfaces provide a novel platform for both scientific studies and applications in biotechnology.

Chiral plasmonic nanocrescents: large-area fabrication and optical properties.

Large-area arrays of substrate-supported plasmonic gold crescents are fabricated by using the new colloidal lithography technique, which is based on an in situ-deposited silica resistance layer. The method provides the means to control the particles' asymmetry just by changing the mutual deposition angle of gold and silica. Asymmetric crescent structures exhibit a pronounced circular dichroism in near-infrared region, with the chiral asymmetry factor reaching 0.2. According to the simulation, the optical chirality enhancement reaches between one and two orders of magnitude and is localized near the crescents' tips.

Podosome Formation and Development in Monocytes Restricted by the Nanoscale Spatial Distribution of ICAM1.

We studied podosome formation and development in activated monocytes (THP1) at ICAM1 (intercellular adhesion molecule 1) nanopatterns of circular and ring-shaped domains and show that cellular binding to a preclustered ICAM1 nanopattern requires ligand patches of at least 200 nm (corresponding to 14 or more integrins). Podosome-like adhesion formation depends on the structure of the ligand pattern under the developing podosome with larger single domains promoting adhesion in a single patch and multiple smaller domains allowing podosome formation by integration of at least 2 smaller domains on either side of the podosome core. Maturation to rosette structures and recruitment of proteases were only observed with macroscopic ICAM1 presentation.

Calcium-phosphate-osteopontin particles for caries control.

Caries is caused by acid production in biofilms on dental surfaces. Preventing caries therefore involves control of microorganisms and/or the acid produced. Here, calcium-phosphate-osteopontin particles are presented as a new approach to caries control. The particles are made by co-precipitation and designed to bind to bacteria in biofilms, impede biofilm build-up without killing the microflora, and release phosphate ions to buffer bacterial acid production if the pH decreases below 6. Analysis of biofilm formation and pH in a five-species biofilm model for dental caries showed that treatment with particles or pure osteopontin led to less biofilm formation compared to untreated controls or biofilms treated with osteopontin-free particles. The anti-biofilm effect can thus be ascribed to osteopontin. The particles also led to a slower acidification of the biofilm after exposure to glucose, and the pH always remained above 5.5. Hence, calcium-phosphate-osteopontin particles show potential for applications in caries control.

Hierarchical protein patterning by meso to molecular scale self-assembly.

Numerous protein patterning methodologies are used extensively for biomedical research and development. We have developed a novel bottom-up protein patterning method using a combination of self-assembly processes in the meso to molecular scale range to allow hierarchical protein patterns to be straightforwardly fabricated with low cost over large areas. As a proof of principle, we patterned vitronectin in various dimensional hierarchies using meso to nanoscale colloids and self-assembled monolayers.

Spatial mapping and quantification of soft and hard protein coronas at silver nanocubes.

Protein coronas around silver nanocubes were quantified in serum-containing media using localized surface plasmon resonances. Both soft and hard coronas showed exposure-time and concentration-dependent changes in protein surface density with time-dependent hardening. We observed spatially dependent kinetics of the corona-formation at cube edges/corners versus facets at short incubation times, where the polymer stabilization agent delayed corona hardening. The soft corona contained more protein than the hard corona at all time-points (8-fold difference with 10% serum conditions).

The nanoscale geometrical maturation of focal adhesions controls stem cell differentiation and mechanotransduction.

We show that the nanoscale adhesion geometry controls the spreading and differentiation of epidermal stem cells. We find that cells respond to such hard nanopatterns similarly to their behavior on soft hydrogels. Cellular responses were seen to stem from local changes in diffusion dynamics of the adapter protein vinculin and associated impaired mechanotransduction rather than impaired recruitment of proteins involved in focal adhesion formation.

From rings to crescents: a novel fabrication technique uncovers the transition details.

A novel fabrication route is reported for the generation of substrate-supported symmetric and asymmetric metal nanostructures. We combine a colloidal template and angled evaporation to deposit in situ mask materials for subsequent lithographic pattern transfer. The technique is demonstrated for the fabrication of concentric and nonconcentric gold rings and crescents. Optical properties of localized plasmon resonances in such structures are studied by UV-vis-NIR spectroscopy and finite-difference time domain simulations during the transition from rings to crescents revealing the development of strong quadrupolar modes.

Onset of bonding plasmon hybridization preceded by gap modes in dielectric splitting of metal disks.

Dielectric splitting of nanoscale disks was studied experimentally and via finite-difference time-domain (FDTD) simulations through systematic introduction of multiple ultrathin dielectric layers. Tunable, hybridized dark bonding modes were seen with first-order gap modes preceding the appearance of bonding dipole-dipole disk modes. The observed bright dipolar mode did not show the energy shift expected from plasmon hybridization but activated dark higher order gap modes. Introducing lateral asymmetry was shown to remodel the field distribution resulting in 3D asymmetry that reoriented the dipole orientation away from the dipole of the elementary disk modes.

Building better habitats: Spatiotemporal signaling cues in 3D biointerfaces for tailored cellular functionality.

A promising research direction in the field of biological engineering is the design and functional programming of three-dimensional (3D) biointerfaces designed to support living cell functionality and growth in vitro, offering a route to precisely regulate cellular behaviors and phenotypes for addressing therapeutic challenges. While traditional two-dimensional (2D) biointerfaces have provided valuable insights, incorporating specific signaling cues into a 3D biointeractive microenvironment at the right locations and time is now recognized as crucial for accurately programming cellular decision-making and communication processes. This approach aims to engineer cell-centric microenvironments with the potential to recapitulate complex biological functions into a finite set of growing cellular organizations. Additionally, they provide insights into the hierarchical logic governing the relationship between molecular components and higher-order multicellular functionality. The functional live cell-based microenvironment engineered through such innovative biointerfaces has the potential to be used as an in vitro model system for expanding our understanding of cellular behaviors or as a therapeutic habitat where cellular functions can be reprogrammed.

Smart Biointerfaces via Click Chemistry-Enabled Nanopatterning of Multiple Bioligands and DNA Force Sensors.

Nanoscale biomolecular placement is crucial for advancing cellular signaling, sensor technology, and molecular interaction studies. Despite this, current methods fall short in enabling large-area nanopatterning of multiple biomolecules while minimizing nonspecific interactions. Using bioorthogonal tags at a submicron scale, we introduce a novel hole-mask colloidal lithography method for arranging up to three distinct proteins, DNA, or peptides on large, fully passivated surfaces. The surfaces are compatible with single-molecule fluorescence microscopy and microplate formats, facilitating versatile applications in cellular and single-molecule assays. We utilize fully passivated and transparent substrates devoid of metals and nanotopographical features to ensure accurate patterning and minimize nonspecific interactions. Surface patterning is achieved using bioorthogonal TCO-tetrazine (inverse electron-demand Diels-Alder, IEDDA) ligation, DBCO-azide (strain-promoted azide-alkyne cycloaddition, SPAAC) click chemistry, and biotin-avidin interactions. These are arranged on surfaces passivated with dense poly(ethylene glycol) PEG brushes crafted through the selective and stepwise removal of sacrificial metallic and polymeric layers, enabling the directed attachment of biospecific tags with nanometric precision. In a proof-of-concept experiment, DNA tension gauge tether (TGT) force sensors, conjugated to cRGD (arginylglycylaspartic acid) in nanoclusters, measured fibroblast integrin tension. This novel application enables the quantification of forces in the piconewton range, which is restricted within the nanopatterned clusters. A second demonstration of the platform to study integrin and epidermal growth factor (EGF) proximal signaling reveals clear mechanotransduction and changes in the cellular morphology. The findings illustrate the platform's potential as a powerful tool for probing complex biochemical pathways involving several molecules arranged with nanometer precision and cellular interactions at the nanoscale.

Versatile Nanoring Fabrication Assisted by Hole-mask Colloidal Lithography.

Nanomaterials shaped as rings are interesting nanostructures with control of the materials properties at the nanoscale. Nanoring plasmonic resonators provide tunable optical resonances in the near-infrared with application in sensing. Fabrication of nanorings can be carried out via top-down approaches based on electron beam lithography with high control of the ring size parameters but at high cost. Alternatively, fabrication via self-assembly approaches has a higher speed/lower cost but at the cost of control of ring parameters. Current colloidal lithography approaches can provide nanoring fabrication over large areas but only of specific materials and a select set of rings (large ring diameters or small rings with ultrathin walls). We extend Hole-mask Colloidal Lithography to use ring shaped holes, allow the deposition of arbitrary materials, and allow the independent tuning of ring-wall thickness over a large range of values. We present a generic approach for the fabrication of nanorings formed from a range of materials including low cost (e.g., Cu, Al) and nonplasmonic (e.g., W) materials and with control of ring wall thickness and diameter allowing tuning of ring parameters and materials for applications in nanooptics and beyond.

Amyloid-ß aggregates activate peripheral monocytes in mild cognitive impairment.

The peripheral immune system is important in neurodegenerative diseases, both in protecting and inflaming the brain, but the underlying mechanisms remain elusive. Alzheimer's Disease is commonly preceded by a prodromal period. Here, we report the presence of large Aß aggregates in plasma from patients with mild cognitive impairment (n = 38). The aggregates are associated with low level Alzheimer's Disease-like brain pathology as observed by 11C-PiB PET and 18F-FTP PET and lowered CD18-rich monocytes. We characterize complement receptor 4 as a strong binder of amyloids and show Aß aggregates are preferentially phagocytosed and stimulate lysosomal activity through this receptor in stem cell-derived microglia. KIM127 integrin activation in monocytes promotes size selective phagocytosis of Aß. Hydrodynamic calculations suggest Aß aggregates associate with vessel walls of the cortical capillaries. In turn, we hypothesize aggregates may provide an adhesion substrate for recruiting CD18-rich monocytes into the cortex. Our results support a role for complement receptor 4 in regulating amyloid homeostasis.

Enhanced refractive index sensitivity of elevated short-range ordered nanohole arrays in optically thin plasmonic Au films.

A simple development of the colloidal lithography technique is demonstrated for fabrication of perforated plasmonic metal films elevated above the substrate surface. The bulk refractive index sensitivity of short-range ordered nanohole arrays in 20 nm thick Au films exhibits an increase of up to 37% due to reduction of substrate effect caused by lifting with a 40 nm silica layer. Analysis of the local electric field distribution suggests that the sensitivity increase is due to revealing of the enhanced field near the holes.

Species differences take shape at nanoparticles: protein corona made of the native repertoire assists cellular interaction.

Cells recognize the biomolecular corona around a nanoparticle, but the biological identity of the complex may be considerably different among various species. This study explores the importance of protein corona composition for nanoparticle recognition by coelomocytes of the earthworm Eisenia fetida using E. fetida coelomic proteins (EfCP) as a native repertoire and fetal bovine serum (FBS) as a non-native reference. We have profiled proteins forming the long-lived corona around silver nanoparticles (75 nm OECD reference materials) and compared the responses of coelomocytes to protein coronas preformed of EfCP or FBS. We find that over time silver nanoparticles can competitively acquire a biological identity native to the cells in situ even in non-native media, and significantly greater cellular accumulation of the nanoparticles was observed with corona complexes preformed of EfCP (p < 0.05). An EfCP-nanoparticle mimicry made with a recombinant protein, lysenin, revealed its critical contribution in the observed cell-nanoparticle response. This confirms the determinant role of the recognizable biological identity during invertebrate in vitro testing of nanoparticles. Our finding shows a case of species-specific formation of biomolecular coronas, and this suggests that the use of representative species may need careful consideration in assessing the risks associated with nanoparticles.

Nanoscale E-cadherin ligand patterns show threshold size for cellular adhesion and adherence junction formation.

The role of ligand spatial distribution on the formation of cadherin mediated cell-cell contacts is studied utilizing nanopatterns of E-cadherin ligands. Protein patches ranging in size from 100 to 800 nm prepared by colloidal lithography critically influence adhesion, spreading, and formation of adherence junctions in epithelial cells. Cells at 100 nm patterns show poor adhesion, while larger pattern sizes show good adhesion, significant spreading, and defined cortical actin. We estimate a threshold of 0.03 µm(2) for epithelial cellular attachment via E-Cadherin.

Serial intravital 2-photon microscopy and analysis of the kidney using upright microscopes.

Serial intravital 2-photon microscopy of the kidney and other abdominal organs is a powerful technique to assess tissue function and structure simultaneously and over time. Thus, serial intravital microscopy can capture dynamic tissue changes during health and disease and holds great potential to characterize (patho-) physiological processes with subcellular resolution. However, successful image acquisition and analysis require significant expertise and impose multiple potential challenges. Abdominal organs are rhythmically displaced by breathing movements which hamper high-resolution imaging. Traditionally, kidney intravital imaging is performed on inverted microscopes where breathing movements are partly compensated by the weight of the animal pressing down. Here, we present a custom and easy-to-implement setup for intravital imaging of the kidney and other abdominal organs on upright microscopes. Furthermore, we provide image processing protocols and a new plugin for the free image analysis software FIJI to process multichannel fluorescence microscopy data. The proposed image processing pipelines cover multiple image denoising algorithms, sample drift correction using 2D registration, and alignment of serial imaging data collected over several weeks using landmark-based 3D registration. The provided tools aim to lower the barrier of entry to intravital microscopy of the kidney and are readily applicable by biomedical practitioners.