Cell-extracellular matrix interactions in the fluidic phase direct the topology and polarity of self-organized epithelial structures.

INTRODUCTION: In vivo, cells are surrounded by extracellular matrix (ECM). To build organs from single cells, it is generally believed that ECM serves as scaffolds to coordinate cell positioning and differentiation. Nevertheless, how cells utilize cell-ECM interactions for the spatiotemporal coordination to different ECM at the tissue scale is not fully understood. METHODS: Here, using in vitro assay with engineered MDCK cells expressing H2B-mCherry (nucleus) and gp135/Podocalyxin-GFP (apical marker), we show in multi-dimensions that such coordination for epithelial morphogenesis can be determined by cell-soluble ECM interaction in the fluidic phase. RESULTS: The coordination depends on the native topology of ECM components such as sheet-like basement membrane (BM) and type I collagen (COL) fibres: scaffold formed by BM (COL) facilitates a close-ended (open-ended) coordination that leads to the formation of lobular (tubular) epithelium. Further, cells form apicobasal polarity throughout the entire lobule/tubule without a complete coverage of ECM at the basal side, and time-lapse two-photon scanning imaging reveals the polarization occurring early and maintained through the lobular expansion. During polarization, gp135-GFP was converged to the apical surface collectively in the lobular/tubular structures, suggesting possible intercellular communications. Under suspension culture, the polarization was impaired with multi-lumen formation in the tubules, implying the importance of ECM biomechanical microenvironment. CONCLUSION: Our results suggest a biophysical mechanism for cells to form polarity and coordinate positioning at tissue scale, and in engineering epithelium through cell-soluble ECM interaction and self-assembly.

ℓ1-regularized maximum likelihood estimation with focused-spot illumination quadruples the diffraction-limited resolution in fluorescence microscopy.

Super-resolution fluorescence microscopy has proven to be a useful tool in biological studies. To achieve more than two-fold resolution improvement over the diffraction limit, existing methods require exploitation of the physical properties of the fluorophores. Recently, it has been demonstrated that achieving more than two-fold resolution improvement without such exploitation is possible using only a focused illumination spot and numerical post-processing. However, how the achievable resolution is affected by the processing step has not been thoroughly investigated. In this paper, we focus on the processing aspect of this emerging super-resolution microscopy technique. Based on a careful examination of the dominant noise source and the available prior information in the image, we find that if a processing scheme is appropriate for the dominant noise model in the image and can utilize the prior information in the form of sparsity, improved accuracy can be expected. Based on simulation results, we identify an improved processing scheme and apply it in a real-world experiment to super-resolve a known calibration sample. We show an improved super-resolution of 60nm, approximately four times beyond the conventional diffraction-limited resolution.

Analyzing the super-resolution characteristics of focused-spot illumination approaches.

SIGNIFICANCE: It is commonly assumed that using the objective lens to create a tightly focused light spot for illumination provides a twofold resolution improvement over the Rayleigh resolution limit and that resolution improvement is independent of object properties. Nevertheless, such an assumption has not been carefully examined. We examine this assumption by analyzing the performance of two super-resolution methods, known as image scanning microscopy (ISM) and illumination-enhanced sparsity (IES). AIM: We aim to identify the fundamental differences between the two methods, and to provide examples that help researchers determine which method to utilize for different imaging conditions. APPROACH: We input the same image datasets into the two methods and analyze their restorations. In numerical simulations, we design objects of distinct brightness and sparsity levels for imaging. We use biological imaging experiments to verify the simulation results. RESULTS: The resolution of IES often exceeds twice the Rayleigh resolution limit when imaging sparse objects. A decrease in object sparsity negatively affects the resolution improvement in both methods. CONCLUSIONS: The IES method is superior for imaging sparse objects with its main features being bright and small against a dark, large background. For objects that are largely bright with small dark features, the ISM method is favorable.

Multiphoton structured thin-plane imaging with a single optical path.

Optical sectioning has become an indispensable technique for high-speed volumetric imaging in the past decade. Here we present a novel optical-sectioning method that produces a thin plane of illumination by exploiting the spatial and temporal properties of multiphoton excitation. Critically, the illumination and detection share the same optical path, as in a conventional epi-fluorescence microscope configuration. Therefore, the imaged sample can be prepared as for standard fluorescence microscopy. Our method also leads to a laterally structured illumination pattern, and this feature can be utilized in structured illumination microscopy to further enhance the imaging performance. We show an example of such an approach, which achieves axial resolution finer than confocal microscopy. We also demonstrate the potential of the new method for biological applications by performing three-dimensional imaging of living Caenorhabditis elegans.

Engineering Improved Antiphosphotyrosine Antibodies Based on an Immunoconvergent Binding Motif.

Phosphotyrosine (pY) is one of the most highly studied posttranslational modifications that is responsible for tightly regulating many signaling pathways in eukaryotes. Pan-specific pY antibodies have emerged as powerful tools for understanding the role of these modifications. Nevertheless, structures have not been reported for pan-specific pY antibodies, greatly impeding the further development of tools for integrating this ubiquitous posttranslational modification using structure-guided designs. Here, we present the first crystal structures of two widely utilized pan-specific pY antibodies, PY20 and 4G10. The two antibodies, although developed independently from animal immunizations, have surprisingly similar modes of recognition of the phosphate group, implicating a generic binding structure among pan-specific pY antibodies. Sequence alignments revealed that many pY binding residues are predominant in the mouse V germline genes, which consequently led to the convergent antibodies. On the basis of the convergent structure, we designed a phage display library by lengthening the CDR-L3 loop with the aid of computational modeling. Panning with this library resulted in a series of 4G10 variants with 4 to 11-fold improvements in pY binding affinities. The crystal structure of one improved variant showed remarkable superposition to the computational model, where the lengthened CDR-L3 loop creates an additional hydrogen bond indirectly bound to the phosphate group via a water molecule. The engineered variants exhibited superior performance in Western blot and immunofluorescence.

Fiber-bundle illumination: realizing high-degree time-multiplexed multifocal multiphoton microscopy with simplicity.

High-degree time-multiplexed multifocal multiphoton microscopy was expected to provide a facile path to scanningless optical-sectioning and the fast imaging of dynamic three-dimensional biological systems. However, physical constraints on typical time multiplexing devices, arising from diffraction in the free-space propagation of light waves, lead to significant manufacturing difficulties and have prevented the experimental realization of high-degree time multiplexing. To resolve this issue, we have developed a novel method using optical fiber bundles of various lengths to confine the diffraction of propagating light waves and to create a time multiplexing effect. Through this method, we experimentally demonstrate the highest degree of time multiplexing ever achieved in multifocal multiphoton microscopy (~50 times larger than conventional approaches), and hence the potential of using simply-manufactured devices for scanningless optical sectioning of biological systems.

Achieving superresolution with illumination-enhanced sparsity.

Recent advances in superresolution fluorescence microscopy have been limited by a belief that surpassing two-fold resolution enhancement of the Rayleigh resolution limit requires stimulated emission or the fluorophore to undergo state transitions. Here we demonstrate a new superresolution method that requires only image acquisitions with a focused illumination spot and computational post-processing. The proposed method utilizes the focused illumination spot to effectively reduce the object size and enhance the object sparsity and consequently increases the resolution and accuracy through nonlinear image post-processing. This method clearly resolves 70nm resolution test objects emitting ~530nm light with a 1.4 numerical aperture (NA) objective, and, when imaging through a 0.5NA objective, exhibits high spatial frequencies comparable to a 1.4NA widefield image, both demonstrating a resolution enhancement above two-fold of the Rayleigh resolution limit. More importantly, we examine how the resolution increases with photon numbers, and show that the more-than-two-fold enhancement is achievable with realistic photon budgets.

Computational design of co-assembling protein-DNA nanowires.

Biomolecular self-assemblies are of great interest to nanotechnologists because of their functional versatility and their biocompatibility. Over the past decade, sophisticated single-component nanostructures composed exclusively of nucleic acids, peptides and proteins have been reported, and these nanostructures have been used in a wide range of applications, from drug delivery to molecular computing. Despite these successes, the development of hybrid co-assemblies of nucleic acids and proteins has remained elusive. Here we use computational protein design to create a protein-DNA co-assembling nanomaterial whose assembly is driven via non-covalent interactions. To achieve this, a homodimerization interface is engineered onto the Drosophila Engrailed homeodomain (ENH), allowing the dimerized protein complex to bind to two double-stranded DNA (dsDNA) molecules. By varying the arrangement of protein-binding sites on the dsDNA, an irregular bulk nanoparticle or a nanowire with single-molecule width can be spontaneously formed by mixing the protein and dsDNA building blocks. We characterize the protein-DNA nanowire using fluorescence microscopy, atomic force microscopy and X-ray crystallography, confirming that the nanowire is formed via the proposed mechanism. This work lays the foundation for the development of new classes of protein-DNA hybrid materials. Further applications can be explored by incorporating DNA origami, DNA aptamers and/or peptide epitopes into the protein-DNA framework presented here.

The wide-field optical sectioning of microlens array and structured illumination-based plane-projection multiphoton microscopy.

We present a theoretical investigation of an optical microscope design that achieves wide-field, multiphoton fluorescence microscopy with finer axial resolution than confocal microscopy. Our technique creates a thin plane of excitation light at the sample using height-staggered microlens arrays (HSMAs), wherein the height staggering of microlenses generate temporal focusing to suppress out-of-focus excitation, and the dense spacing of microlenses enables the implementation of structured illumination technique to eliminate residual out-of-focus signal. We use physical optics-based numerical simulations to demonstrate that our proposed technique can achieve diffraction-limited three-dimensional imaging through a simple optical design.

Long-range mechanical force enables self-assembly of epithelial tubular patterns.

Enabling long-range transport of molecules, tubules are critical for human body homeostasis. One fundamental question in tubule formation is how individual cells coordinate their positioning over long spatial scales, which can be as long as the sizes of tubular organs. Recent studies indicate that type I collagen (COL) is important in the development of epithelial tubules. Nevertheless, how cell-COL interactions contribute to the initiation or the maintenance of long-scale tubular patterns is unclear. Using a two-step process to quantitatively control cell-COL interaction, we show that epithelial cells developed various patterns in response to fine-tuned percentages of COL in ECM. In contrast with conventional thoughts, these patterns were initiated and maintained by traction forces created by cells but not diffusive factors secreted by cells. In particular, COL-dependent transmission of force in the ECM led to long-scale (up to 600 µm) interactions between cells. A mechanical feedback effect was encountered when cells used forces to modify cell positioning and COL distribution and orientations. Such feedback led to a bistability in the formation of linear, tubule-like patterns. Using micro-patterning technique, we further show that the stability of tubule-like patterns depended on the lengths of tubules. Our results suggest a mechanical mechanism that cells can use to initiate and maintain long-scale tubular patterns.

Wide-field optical sectioning for live-tissue imaging by plane-projection multiphoton microscopy.

Optical sectioning provides three-dimensional (3D) information in biological tissues. However, most imaging techniques implemented with optical sectioning are either slow or deleterious to live tissues. Here, we present a simple design for wide-field multiphoton microscopy, which provides optical sectioning at a reasonable frame rate and with a biocompatible laser dosage. The underlying mechanism of optical sectioning is diffuser-based temporal focusing. Axial resolution comparable to confocal microscopy is theoretically derived and experimentally demonstrated. To achieve a reasonable frame rate without increasing the laser power, a low-repetition-rate ultrafast laser amplifier was used in our setup. A frame rate comparable to that of epifluorescence microscopy was demonstrated in the 3D imaging of fluorescent protein expressed in live epithelial cell clusters. In this report, our design displays the potential to be widely used for video-rate live-tissue and embryo imaging with axial resolution comparable to laser scanning microscopy.

Second harmonic generation imaging - a new method for unraveling molecular information of starch.

We present a new method, second harmonic generation (SHG) imaging for the study of starch structure. SHG imaging can provide the structural organization and molecular orientation information of bio-tissues without centrosymmetry. In recent years, SHG has proven its capability in the study of crystallized bio-molecules such as collagen and myosin. Starch, the most important food source and a promising future energy candidate, has, for a decade, been shown to exhibit strong SHG response. By comparing SHG intensity from different starch species, we first identified that the SHG-active molecule is amylopectin, which accounts for the crystallinity in starch granules. With the aid of SHG polarization anisotropy, we extracted the complete χ((2)) tensor of amylopectin, which reflects the underlying molecular details. Through χ((2)) tensor analysis, three-dimensional orientation and packing symmetry of amylopectin are determined. The helical angle of the double-helix in amylopectin is also deduced from the tensor, and the value corresponds well to previous X-ray studies, further verifying amylopectin as SHG source. It is noteworthy that the nm-sized structure of amylopectin inside a starch granule can be determined by this far-field optical method with 1-µm excitation wavelength. Since SHG is a relatively new tool for plant research, a detailed understanding of SHG in starch structure will be useful for future high-resolution imaging and quantitative analyses for food/energy applications.

A diffraction-limited scanning system providing broad spectral range for laser scanning microscopy.

Diversified research interests in scanning laser microscopy nowadays require broadband capability of the optical system. Although an all-mirror-based optical design with a suitable metallic coating is appropriate for broad-spectrum applications from ultraviolet to terahertz, most researchers prefer lens-based scanning systems despite the drawbacks of a limited spectral range, ghost reflection, and chromatic aberration. One of the main concerns is that the geometrical aberration induced by off-axis incidence on spherical mirrors significantly deteriorates image resolution. Here, we demonstrate a novel geometrical design of a spherical-mirror-based scanning system in which off-axis aberrations, both astigmatism and coma, are compensated to reach diffraction-limited performance. We have numerically simulated and experimentally verified that this scanning system meets the Marechal condition and provides high Strehl ratio within a 3 degrees x 3 degrees scanning area. Moreover, we demonstrate second-harmonic-generation imaging from starch with our new design. A greatly improved resolution compared to the conventional mirror-based system is confirmed. This scanning system will be ideal for high-resolution linear/nonlinear laser scanning microscopy, ophthalmoscopic applications, and precision fabrications.