Beyond the diffraction limit?

Highly Accurate Profiling of Exosome Phenotypes Using Super-resolution Tricolor Fluorescence Co-localization

Exosomes contain a wealth of proteomic information, presenting promising biomarkers for the noninvasive early diagnosis of diseases, especially cancer. However, it remains a great challenge to accurately and reliably distinguish exosomes secreted from different types of cell lines. Fluorescence immunoassay is frequently used for exosome detection. Nonspecific adsorption in immunoassays is unavoidable and affects the reliability of assay results. Despite the fact that various methods have been proposed to reduce nonspecific adsorption, a more effective method that can eliminate the influence of nonspecific adsorption is still lacking. Here, we report a more convenient way (named SR-TFC) to remove the artifacts caused by nonspecific adsorption, which combines tricolor fluorescence labeling of target exosomes, tricolor super-resolution imaging, and pixel counting. The pixel counting method (named CFPP) is realized by MATLAB and can eliminate nonspecific binding sites at the single-pixel level, which has never been achieved before and could improve the reliability of detection to the maximum extent. Furthermore, as a proof-of-concept, profiling of exosomal membrane proteins and identification of breast cancer subpopulations are demonstrated. To enable multiplex breast cancer phenotypic analysis, three kinds of specific proteins are labeled to obtain the 3D phenotypic information on various exosomes. Breast cancer subtypes can be accurately identified according to the super-resolution images of some clinically relevant exosomal proteins. Worth mentioning is that, by selecting other biomarkers, classification of other cancers could also be realized using SR-TFC. Hence, the present work holds great potential in clinical cancer diagnosis and precision medicine.

Near-Infrared Perylenecarboximide Fluorophores for Live-Cell Super-Resolution Imaging

Organic near-infrared (NIR) photoblinking fluorophores are highly desirable for live-cell super-resolution imaging based on single-molecule localization microscopy (SMLM). Herein we introduce a novel small chromophore, PMIP, through the fusion of perylenecarboximide with 2,2-dimetheylpyrimidine. PMIP exhibits an emission maximum at 732 nm with a high fluorescence quantum yield of 60% in the wavelength range of 700-1000 nm and excellent photoblinking without any additives. With resorcinol-functionalized PMIP (PMIP-OH), NIR SMLM imaging of lysosomes is demonstrated for the first time in living mammalian cells under physiological conditions. Moreover, metabolically labeled nascent DNA is site-specifically detected using azido-functionalized PMIP (PMIP-N3) via click chemistry, thereby enabling the super-resolution imaging of nascent DNA in phosphate-buffered saline with a 9-fold improvement in spatial resolution. These results indicate the potential of PMIP-based NIR blinking fluorophores for biological applications of SMLM.

An acoustofluidic scanning nanoscope using enhanced image stacking and processing

Nanoscale optical resolution with a large field of view is a critical feature for many research and industry areas, such as semiconductor fabrication, biomedical imaging, and nanoscale material identification. Several scanning microscopes have been developed to resolve the inverse relationship between the resolution and field of view; however, those scanning microscopes still rely upon fluorescence labeling and complex optical systems. To overcome these limitations, we developed a dual-camera acoustofluidic nanoscope with a seamless image merging algorithm (alpha-blending process). This design allows us to precisely image both the sample and the microspheres simultaneously and accurately track the particle path and location. Therefore, the number of images required to capture the entire field of view (200 × 200 μm) by using our acoustofluidic scanning nanoscope is reduced by 55-fold compared with previous designs. Moreover, the image quality is also greatly improved by applying an alpha-blending imaging technique, which is critical for accurately depicting and identifying nanoscale objects or processes. This dual-camera acoustofluidic nanoscope paves the way for enhanced nanoimaging with high resolution and a large field of view.

Leaf microscopy applications in photosynthesis research: identifying the gaps

Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure-function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.

Super-resolution mid-infrared spectro-microscopy of biological applications through tapping mode and peak force tapping mode atomic force microscope

Small biomolecules at the subcellular level are building blocks for the manifestation of complex biological activities. However, non-intrusive in situ investigation of biological systems has been long daunted by the low spatial resolution and poor sensitivity of conventional light microscopies. Traditional infrared (IR) spectro-microscopy can enable label-free visualization of chemical bonds without extrinsic labeling but is still bound by Abbe's diffraction limit. This review article introduces a way to bypass the optical diffraction limit and improve the sensitivity for mid-IR methods - using tip-enhanced light nearfield in atomic force microscopy (AFM) operated in tapping and peak force tapping modes. Working principles of well-established scattering-type scanning near-field optical microscopy (s-SNOM) and two relatively new techniques, namely, photo-induced force microscopy (PiFM) and peak force infrared (PFIR) microscopy, will be briefly presented. With ∼ 10-20 nm spatial resolution and monolayer sensitivity, their recent applications in revealing nanoscale chemical heterogeneities in a wide range of biological systems, including biomolecules, cells, tissues, and biomaterials, will be reviewed and discussed. We also envision several future improvements of AFM-based tapping and peak force tapping mode nano-IR methods that permit them to better serve as a versatile platform for uncovering biological mechanisms at the fundamental level.

Numerical investigation of a light delivery device using metal/insulator/metal with a 3D linear taper waveguide and an input grating for heat-assisted magnetic recording

Heat-assisted magnetic recording (HAMR), a new technique to overcome the data-density limitation, uses a laser to temporarily heat a nanovolume of a recording medium. Thus, this paper proposes a light delivery device that uses the metal/insulator/metal waveguide with a three-dimensional linear taper, and a grating added for an input, for HAMR. Our structure was calculated by finite-element method simulation. By design, 830 nm of light was delivered into a 50nm² spot area with 63% coupling efficiency, and power intensity was enhanced 930 times. This achievement potential could be applied to the HAMR system in the future.

The Expanding Frontiers of Tip-Enhanced Raman Spectroscopy

Fundamental understanding of chemistry and physical properties at the nanoscale enables the rational design of interface-based systems. Surface interactions underlie numerous technologies ranging from catalysis to organic thin films to biological systems. Since surface environments are especially prone to heterogeneity, it becomes crucial to characterize these systems with spatial resolution sufficient to localize individual active sites or defects. Spectroscopy presents as a powerful means to understand these interactions, but typical light-based techniques lack sufficient spatial resolution. This review describes the growing number of applications for the nanoscale spectroscopic technique, tip-enhanced Raman spectroscopy (TERS), with a focus on developments in areas that involve measurements in new environmental conditions, such as liquid, electrochemical, and ultrahigh vacuum. The expansion into unique environments enables the ability to spectroscopically define chemistry at the spatial limit. Through the confinement and enhancement of light at the apex of a plasmonic scanning probe microscopy tip, TERS is able to yield vibrational fingerprint information of molecules and materials with nanoscale resolution, providing insight into highly localized chemical effects.

Fluorescent Probes for Super-Resolution Microscopy of Lysosomes

Lysosomes are membrane-enclosed small spherical cytoplasmic organelles. Malfunctioning and abnormalities in lysosomes can cause a plethora of neurodegenerative diseases. Consequently, understanding the structural information on lysosomes down to a subnanometer level is essential. Recently, super-resolution imaging techniques enable us to visualize dynamical processes occurring in suborganelle structures inside living cells down to subnanometer accuracy by breaking the diffraction limit. A brighter and highly photostable fluorescent probe is essential for super-resolution microscopy. In this regard, this mini-review deals with the various types of super-resolution techniques and the probes that are used to specifically stain and resolve the structure of the lysosomes.

On the actual spatial resolution of Brillouin Imaging

Brillouin imaging is an emerging optical elastography technique that is able to generate maps of the mechanical properties at microscale with great potential in biophysical and biomedical fields. A key parameter is its spatial resolution, which is usually identified with that of the confocal microscope coupled to the Brillouin interferometer. Conversely, here we demonstrate that the mean free path of acoustic phonons plays a major role in defining the resolution, especially for high numerical aperture confocal setups. Surprisingly, the resolution of elastography maps may even deteriorate when decreasing the scattering volume.

Refining particle positions using circular symmetry

Particle and object tracking is gaining attention in industrial applications and is commonly applied in: colloidal, biophysical, ecological, and micro-fluidic research. Reliable tracking information is heavily dependent on the system under study and algorithms that correctly determine particle position between images. However, in a real environmental context with the presence of noise including particular or dissolved matter in water, and low and fluctuating light conditions, many algorithms fail to obtain reliable information. We propose a new algorithm, the Circular Symmetry algorithm (C-Sym), for detecting the position of a circular particle with high accuracy and precision in noisy conditions. The algorithm takes advantage of the spatial symmetry of the particle allowing for subpixel accuracy. We compare the proposed algorithm with four different methods using both synthetic and experimental datasets. The results show that C-Sym is the most accurate and precise algorithm when tracking micro-particles in all tested conditions and it has the potential for use in applications including tracking biota in their environment.

Enhanced Performance of Blended Polymer Excipients in Delivering a Hydrophobic Drug through the Synergistic Action of Micelles and HPMCAS

Blends of hydroxypropyl methylcellulose acetate succinate (HPMCAS) and dodecyl (C₁₂)-tailed poly(N-isopropylacrylamide) (PNIPAm) were systematically explored as a model system to dispense the active ingredient phenytoin by rapid dissolution, followed by the suppression of drug crystallization for an extended period. Dynamic and static light scattering revealed that C₁₂-PNIPAm polymers, synthesized by reversible addition-fragmentation chain-transfer polymerization, self-assembled into micelles with dodecyl cores in phosphate-buffered saline (PBS, pH 6.5). A synergistic effect on drug supersaturation was documented during in vitro dissolution tests by varying the blending ratio, with HPMACS primarily aiding in rapid dissolution and PNIPAm maintaining supersaturation. Polarized light and cryogenic transmission electron microscopy experiments revealed that C₁₂-PNIPAm micelles maintain drug supersaturation by inhibiting both crystal nucleation and growth. Cross-peaks between the phenyl group of phenytoin and the isopropyl group of C₁₂-PNIPAm in 2D ¹H nuclear Overhauser effect (NOESY) spectra confirmed the existence of drug-polymer intermolecular interactions in solution. Phenytoin and polymer diffusion coefficients, measured by diffusion-ordered NMR spectroscopy (DOSY), demonstrated that the drug-polymer association constant increased with increasing local density of the corona chains, coincident with a reduction in C₁₂-PNIPAm molecular weight. These findings demonstrate a new strategy for exploiting the versatility of polymer blends through the use of self-assembled micelles in the design of advanced excipients.

Internal rib structure can be predicted using mathematical models: An anatomic study comparing the chest to a shell dome with application to understanding fractures

The human rib cage resembles a masonry dome in shape. Masonry domes have a particular construction that mimics stress distribution. Rib cortical thickness and bone density were analyzed to determine whether the morphology of the rib cage is sufficiently similar to a shell dome for internal rib structure to be predicted mathematically. A finite element analysis (FEA) simulation was used to measure stresses on the internal and external surfaces of a chest-shaped dome. Inner and outer rib cortical thickness and bone density were measured in the mid-axillary lines of seven cadaveric rib cages using computerized tomography scanning. Paired t tests and Pearson correlation were used to relate cortical thickness and bone density to stress. FEA modeling showed that the stress was 82% higher on the internal than the external surface, with a gradual decrease in internal and external wall stresses from the base to the apex. The inner cortex was more radio-dense, P < 0.001, and thicker, P < 0.001, than the outer cortex. Inner cortical thickness was related to internal stress, r = 0.94, P < 0.001, inner cortical bone density to internal stress, r = 0.87, P = 0.003, and outer cortical thickness to external stress, r = 0.65, P = 0.035. Mathematical models were developed relating internal and external cortical thicknesses and bone densities to rib level. The internal anatomical features of ribs, including the inner and outer cortical thicknesses and bone densities, are similar to the stress distribution in dome-shaped structures modeled using FEA computer simulations of a thick-walled dome pressure vessel. Fixation of rib fractures should include the stronger internal cortex.

Note: Fabrication of resolution target for super-resolution microscopy

We fabricated a resolution target for super-resolution microscopes (SRMs). The target was constructed by scattering a dyed photo-resist on a glass cover plate and used UV nano-imprinting to transfer minute line-and-space patterns on to the photo-resist layer. Using this resolution target, an image obtained from a SRM and its properties was evaluated quantitatively.

Quantitative biology of single neurons

The building blocks of complex biological systems are single cells. Fundamental insights gained from single-cell analysis promise to provide the framework for understanding normal biological systems development as well as the limits on systems/cellular ability to respond to disease. The interplay of cells to create functional systems is not well understood. Until recently, the study of single cells has concentrated primarily on morphological and physiological characterization. With the application of new highly sensitive molecular and genomic technologies, the quantitative biochemistry of single cells is now accessible.

Optimal design of composite nanowires for extended reach of surface plasmon-polaritons

We theoretically investigate composite cylindrical nanowires for the waveguiding of the lowest-order surface plasmon-polariton (SPP) mode. We find that the confinement of the SPP fields in a metallic nanowire can be significantly improved by a dielectric cladding and show that by adjusting the thickness of the optically-pumped cladding, the gain required to compensate for the losses can be minimized. If this structure is coated with an additional metal layer to form a metal-dielectric-metal (MDM) nanowire, we show that the field can be predominantly confined within the dielectric layer, to have amplitudes of three orders of magnitude higher than those in the metallic regions. We also show that the propagation lengths of SPPs can be maximized by the proper selection of the geometrical parameters. We further demonstrate that the mode is strongly confined in subwavelength scale, e.g., ∼λ(0)(2)/1220 for a 60-nm-thick nanowire, where λ(0) is the wavelength in vacuum. We also find that regardless of the size of nanowire, it is possible to carry over 98.5% of the mode energy within the nanowire. In addition, we demonstrate that by appropriate choice of the material thicknesses, the losses of an MDM nanowire can be compensated by a considerably low level of optical gain in the dielectric region. For example, the losses of a 260-nm-thick Ag-ZnO-Ag nanowire can be entirely compensated by a gain of ∼ 400 cm(-1). Our results will be useful for the optimum design of nanowires as interconnects for high-density nanophotonic circuit integration.

Studies on structures of lipid A-monophosphate clusters

Single crystalline clusters of lipid A-monophosphate were grown from organic dispersions containing 5-15% (v/v) water at various volume fractions, φ, and temperatures. The morphology of the single lipid A-monophosphate crystals was either rhombohedral or hexagonal. The hexagonal crystals were needlelike or cylindrical in shape, with the long dimension parallel to the c axis of the unit cell. The crystalline clusters were studied using electron microscopy and x-ray powder diffraction. Employing molecular location methods following a Rietveld refinement and whole-pattern refinement revealed two monoclinic crystal structures in the space groups P2(1) and C2, both converged with R(F) = 0.179. The two monoclinic crystal structures were packing (hydrocarbon chains) and conformational (sugar) polymorphs. Neither of these two structures had been encountered previously. Only intramolecular hydrogen bonding was observed for the polymorphs, which were located between the amide and the carboxyl groups. Another crystalline structure was found in the volume-fraction range 2.00 × 10(-3) ≤ φ ≤ 2.50 × 10(-3), which displayed hexagonal symmetry. The hexagonal symmetry of the self-assembled lipid A-monophosphate crystalline phase might be reconciled with the monoclinic symmetry found at low-volume-fractions. Therefore, lowering the symmetry from cubic, i.e., Ia 3d, to rhombohedral R 3 m, and finally to the monoclinic space group C2 was acceptable if the lipid A-monophosphate anion was completely orientationally ordered.

Imaging

Science would be so much easier if we could actually see what the atoms and molecules looked like. So what's stopping us? In this chapter (and the next) we take a look at the ways in which we might visualize the structures of objects at the microscopic level and beyond.

Is too 'creative' language acceptable in crystallography?

A brief comment is made on the need to use carefully selected, novel terms in crystallographic publications, especially publications addressing non-specialists.

While figures of speech are often useful and even educational, flashy titles combined with hyperbolae and imprecise language can mislead or deceive non-specialist readers and should therefore be avoided. The possibility of such confusion exists when poorly defined terms like ‘structure quality’ or ‘super-resolution’ are used to describe a protein structure.

The challenges of sequencing by synthesis

DNA sequencing-by-synthesis (SBS) technology, using a polymerase or ligase enzyme as its core biochemistry, has already been incorporated in several second-generation DNA sequencing systems with significant performance. Notwithstanding the substantial success of these SBS platforms, challenges continue to limit the ability to reduce the cost of sequencing a human genome to $100,000 or less. Achieving dramatically reduced cost with enhanced throughput and quality will require the seamless integration of scientific and technological effort across disciplines within biochemistry, chemistry, physics and engineering. The challenges include sample preparation, surface chemistry, fluorescent labels, optimizing the enzyme-substrate system, optics, instrumentation, understanding tradeoffs of throughput versus accuracy, and read-length/phasing limitations. By framing these challenges in a manner accessible to a broad community of scientists and engineers, we hope to solicit input from the broader research community on means of accelerating the advancement of genome sequencing technology.

Beyond the diffraction limit: far-field fluorescence imaging with ultrahigh resolution

Fluorescence microscopy is an important and extensively utilised tool for imaging biological systems. However, the image resolution that can be obtained has a limit as defined through the laws of diffraction. Demand for improved resolution has stimulated research into developing methods to image beyond the diffraction limit based on far-field fluorescence microscopy techniques. Rapid progress is being made in this area of science with methods emerging that enable fluorescence imaging in the far-field to possess a resolution well beyond the diffraction limit. This review outlines developments in far-field fluorescence methods which enable ultrahigh resolution imaging and application of these techniques to biology. Future possible trends and directions in far-field fluorescence imaging with ultrahigh resolution are also outlined.

Measurement of contrast transfer function in super-resolution microscopy using two-color fluorescence dip spectroscopy

The contrast transfer function (CTF) of super-resolution microscopy was quantitatively investigated using a fluorescent scale. The scale has minute fluorescent line patterns, finer than 100 nm, and is suitable for measuring CTF in super-resolution microscopy. The measured CTF shows that super-resolution microscopy can indeed improve the optical properties of fluorescent images and enable us to observe a structure with the spatial resolution overcoming the diffraction limit. From the CTF, it has been found that super-resolution microcopy can resolve a 100 nm line-and-space pattern and provides a contrast of 10%. The CTF corresponds to a PSF with a full-width at half-maximum (FWHM) of 130 nm. An evaluation using a 100 nmphi fluorescent bead consistently supports the results given by the CTF for super-resolution microscopy.

Two-point separation in far-field super-resolution fluorescence microscopy based on two-color fluorescence dip spectroscopy, Part I: Experimental evaluation

The two-point resolution of a novel two-color far-field super-resolution fluorescence microscopy was evaluated by measuring fluorescent beads 100 nm in diameter. This microscopy is based on a combination of two-color fluorescence dip spectroscopy and a phase-modulation technique for a laser beam. By simply introducing two-color laser light, the size of the fluorescent image of a bead was shrunk down to a diameter of 250 nm from the diffraction-limited image with a diameter of 360 nm. For two closely adjacent fluorescent beads with a separation distance of 350 nm, the two-color microscope clearly gave separated fluorescence images, while the conventional one-color fluorescence microscope could not resolve them. It has been proved that our technique breaks Rayleigh's diffraction limit.

Mitochondrial localization as a determinant of capacitative Ca2+ entry in HeLa cells

Whether different subsets of mitochondria play distinct roles in shaping intracellular Ca2+ signals is presently unresolved. Here, we determine the role of mitochondria located beneath the plasma membrane in controlling (a) Ca2+ release from the endoplasmic reticulum (ER) and (b) capacitative Ca2+ entry. By over-expression of the dynactin subunit dynamitin, and consequent inhibition of the fission factor, dynamin-related protein (Drp-1), mitochondria were relocalised from the plasma membrane towards the nuclear periphery in HeLa cells. The impact of these changes on free calcium concentration in the cytosol ([Ca2+]c), mitochondria ([Ca2+]m) and ER ([Ca2+]ER) was then monitored with specifically-targeted aequorins. Whilst dynamitin over-expression increased the number of close contacts between the ER and mitochondria by >2.5-fold, assessed using organelle-targeted GFP variants, histamine-induced changes in organellar [Ca2+] were unaffected. By contrast, Ca2+ influx elicited significantly smaller increases in [Ca2+]c and [Ca2+]m in dynamitin-expressing than in control cells. These data suggest that the strategic localisation of a subset of mitochondria beneath the plasma membrane is required for normal Ca2+ influx, but that the transfer of Ca2+ ions between the ER and mitochondria is relatively insensitive to gross changes in the spatial relationship between these two organelles.

Reconstruction of spatial, phase, and coherence properties of light

Image reconstruction of partially coherent light is interpreted as quantum-state reconstruction. An efficient method based on the maximum-likelihood estimation is proposed for acquiring information from blurred intensity measurements affected by noise. Connections with incoherent-image restoration are pointed out. The feasibility of the method is demonstrated numerically. Spatial and correlation details significantly below the diffraction limit are revealed in the reconstructed pattern.

Light microscopy techniques for live cell imaging

Since the earliest examination of cellular structures, biologists have been fascinated by observing cells using light microscopy. The advent of fluorescent labeling technologies plus the plethora of sophisticated light microscope techniques now available make studying dynamic processes in living cells almost commonplace. For anyone new to this area, however, it can be daunting to decide which techniques or equipment to try. Here, we aim to give a brief overview of the main approaches to live cell imaging, with some mention of their pros and cons.