Hydrogel-Tissue Chemistry: Principles and Applications

Towards developing a matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) compatible tissue expansion protocol

Mass spectrometry imaging (MSI) visualizes spatial distribution of molecules in a biological tissue. However, compared with traditional microscopy-based imaging, conventional MSI is limited to its spatial resolution, resulting in difficulties in identifying detailed tissue morphological characters, such as lesion boundary or nanoscale structures. On the other hand, expansion microscopy, a tissue expansion method widely used in optical imaging to improve morphological details, has great potential to solve insufficient spatial resolution in mass spectrometry imaging (MSI). However, expansion microscopy was not originally designed for MSI, resulting in problems while combining expansion microscopy and MSI such as expanded sample fragility, vacuum stability and molecule loss during sample preparation. In this research we developed a MALDI MSI compatible expansion protocol by adjusting sample preparation methods during tissue expansion, successfully combining expansion microscopy with MSI. After tissue expansion the expanded sample can be readily applied to MALDI MSI sample preparation and further data acquisition. The MALDI MSI compatible expansion protocol has great potential to be widely applied in MALDI MSI sample preparation to facilitate improvement of MSI spatial resolution.

Metal nanoparticle hybrid hydrogels: the state-of-the-art of combining hard and soft materials to promote wound healing

Wounds represent a grave affliction that profoundly impacts human well-being. Establishing barriers, preventing infections, and providing a conducive microenvironment constitute the crux of wound therapy. Hydrogel, a polymer with an intricate three-dimensional lattice, serves as a potent tool in erecting physical barriers and nurturing an environment conducive to wound healing. This enables effective control over exudation, hemostasis, accelerated wound closure, and diminished scar formation. As a result, hydrogels have gained extensive traction in the realm of wound treatment. Metallic nanoparticle carriers, characterized by their multifaceted responses encompassing acoustics, optics, and electronics, have demonstrated efficacy in wound management. Nevertheless, these carriers encounter challenges associated with swift clearance and nonuniform effectiveness. The hybridization of metallic nanoparticle carriers with hydrogels overcomes the shortcomings inherent in metallic nanoparticle-based wound therapy. This amalgamation not only addresses the limitations but also augments the mechanical robustness of hydrogels. It confers upon them attributes such as environmental responsiveness and multifunctionality, thereby synergizing strengths and compensating for weaknesses. This integration culminates in the precise and intelligent management of wounds. This review encapsulates the structural classifications, design strategies, therapeutic applications, and underlying mechanisms of metal nanoparticle hybrid hydrogels in the context of acute and chronic wound treatment. The discourse delves into the generation of novel or enhanced attributes arising from hybridization and how the current paradigm of wound therapy leverages these attributes. Amidst this continually evolving frontier, the potential of metal nanoparticle hybrid hydrogels to revolutionize wound treatment is underscored.

Biomaterials in Traumatic Brain Injury: Perspectives and Challenges

Traumatic brain injury (TBI) is a leading cause of mortality and long-term impairment globally. TBI has a dynamic pathology, encompassing a variety of metabolic and molecular events that occur in two phases: primary and secondary. A forceful external blow to the brain initiates the primary phase, followed by a secondary phase that involves the release of calcium ions (Ca2+) and the initiation of a cascade of inflammatory processes, including mitochondrial dysfunction, a rise in oxidative stress, activation of glial cells, and damage to the blood-brain barrier (BBB), resulting in paracellular leakage. Currently, there are no FDA-approved drugs for TBI, but existing approaches rely on delivering micro- and macromolecular treatments, which are constrained by the BBB, poor retention, off-target toxicity, and the complex pathology of TBI. Therefore, there is a demand for innovative and alternative therapeutics with effective delivery tactics for the diagnosis and treatment of TBI. Tissue engineering, which includes the use of biomaterials, is one such alternative approach. Biomaterials, such as hydrogels, including self-assembling peptides and electrospun nanofibers, can be used alone or in combination with neuronal stem cells to induce neurite outgrowth, the differentiation of human neural stem cells, and nerve gap bridging in TBI. This review examines the inclusion of biomaterials as potential treatments for TBI, including their types, synthesis, and mechanisms of action. This review also discusses the challenges faced by the use of biomaterials in TBI, including the development of biodegradable, biocompatible, and mechanically flexible biomaterials and, if combined with stem cells, the survival rate of the transplanted stem cells. A better understanding of the mechanisms and drawbacks of these novel therapeutic approaches will help to guide the design of future TBI therapies.

Deep learning-driven adaptive optics for single-molecule localization microscopy

The inhomogeneous refractive indices of biological tissues blur and distort single-molecule emission patterns generating image artifacts and decreasing the achievable resolution of single-molecule localization microscopy (SMLM). Conventional sensorless adaptive optics methods rely on iterative mirror changes and image-quality metrics. However, these metrics result in inconsistent metric responses and thus fundamentally limit their efficacy for aberration correction in tissues. To bypass iterative trial-then-evaluate processes, we developed deep learning-driven adaptive optics for SMLM to allow direct inference of wavefront distortion and near real-time compensation. Our trained deep neural network monitors the individual emission patterns from single-molecule experiments, infers their shared wavefront distortion, feeds the estimates through a dynamic filter and drives a deformable mirror to compensate sample-induced aberrations. We demonstrated that our method simultaneously estimates and compensates 28 wavefront deformation shapes and improves the resolution and fidelity of three-dimensional SMLM through >130-µm-thick brain tissue specimens.

Spatial transcriptomics in neuroscience

The brain is one of the most complex living tissue types and is composed of an exceptional diversity of cell types displaying unique functional connectivity. Single-cell RNA sequencing (scRNA-seq) can be used to efficiently map the molecular identities of the various cell types in the brain by providing the transcriptomic profiles of individual cells isolated from the tissue. However, the lack of spatial context in scRNA-seq prevents a comprehensive understanding of how different configurations of cell types give rise to specific functions in individual brain regions and how each distinct cell is connected to form a functional unit. To understand how the various cell types contribute to specific brain functions, it is crucial to correlate the identities of individual cells obtained through scRNA-seq with their spatial information in intact tissue. Spatial transcriptomics (ST) can resolve the complex spatial organization of cell types in the brain and their connectivity. Various ST tools developed during the past decade based on imaging and sequencing technology have permitted the creation of functional atlases of the brain and have pulled the properties of neural circuits into ever-sharper focus. In this review, we present a summary of several ST tools and their applications in neuroscience and discuss the unprecedented insights these tools have made possible.

Polymeric Based Hydrogel Membranes for Biomedical Applications

The development of biomedical applications is a transdisciplinary field that in recent years has involved researchers from chemistry, pharmacy, medicine, biology, biophysics, and biomechanical engineering. The fabrication of biomedical devices requires the use of biocompatible materials that do not damage living tissues and have some biomechanical characteristics. The use of polymeric membranes, as materials meeting the above-mentioned requirements, has become increasingly popular in recent years, with outstanding results in tissue engineering, for regeneration and replenishment of tissues constituting internal organs, in wound healing dressings, and in the realization of systems for diagnosis and therapy, through the controlled release of active substances. The biomedical application of hydrogel membranes has had little uptake in the past due to the toxicity of cross-linking agents and to the existing limitations regarding gelation under physiological conditions, but now it is proving to be a very promising field This review presents the important technological innovations that the use of membrane hydrogels has promoted, enabling the resolution of recurrent clinical problems, such as post-transplant rejection crises, haemorrhagic crises due to the adhesion of proteins, bacteria, and platelets on biomedical devices in contact with blood, and poor compliance of patients undergoing long-term drug therapies.

Role of nano-hydrogels coated exosomes in bone tissue repair

With the development of nanotechnology, nanomaterials are widely applied in different areas. Some nanomaterials are designed to be biocompatible and can be used in the medical field, playing an important role in disease treatment. Exosomes are nanoscale vesicles with a diameter of 30-200 nm. Studies have shown that exosomes have the effect of angiogenesis, tissue (skin, tendon, cartilage, et al.) repair and reconstruction. Nano-hydrogels are hydrogels with a diameter of 200 nm or less and can be used as the carrier to transport the exosomes into the body. Some orthopedic diseases, such as bone defects and bone infections, are difficult to handle. The emergence of nano-hydrogels coated exosomes may provide a new idea to solve these problems, improving the prognosis of patients. This review summarizes the function of nano-hydrogels coated exosomes in bone tissue repair, intending to illustrate the potential use and application of nano-hydrogels coated exosomes in bone disease.

Hydrogels as the plant culture substrates: A review

A class of hydrophilic polymers known as "hydrogels" have extensive water content and three-dimensional crosslinked networks. Since the old period, they have been utilized as plant culture substrates to get around the drawbacks of hydroponics and soil. Numerous hydrogels, particularly polysaccharides with exceptional stability, high clarity, and low cost can be employed as plant substrates. Although numerous novel and functionalized hydrogels might assist in overcoming the drawbacks of conventional media and giving them more functions, the existing hydrogel-based plant growth substrates rarely benefit from the developments of gels in the previous few decades. Prospects include the development of new conduction techniques, the creation of potential new hydrogels, and the functionalization of the hydrogel as plant culture substrates.

Volumetric imaging of optically cleared and fluorescently labeled animal tissue (VIOLA) for quantifying the 3D biodistribution of nanoparticles at cellular resolution in tumor tissue

Nanoparticle (NP) technology holds significant promise to mediate targeted drug delivery to specific organs in the body. Understanding the 3D biodistribution of NPs in heterogeneous environments such as the tumor tissue can provide crucial information on efficacy, safety and potential clinical outcomes. Here we present a novel end-to-end workflow, VIOLA, which makes use of tissue clearing methodology in conjunction with high resolution imaging and advanced 3D image processing to quantify the spatiotemporal 3D biodistribution of fluorescently labeled ACCURIN® NPs. Specifically, we investigate the spatiotemporal biodistribution of NPs in three different murine tumor models (CT26, EMT6, and KPC-GEM) of increasing complexity and translational relevance. We have developed new endpoints to characterize NP biodistribution at multiple length scales. Our observations reveal that the macroscale NP biodistribution is spatially heterogeneous and exhibits a gradient with relatively high accumulation at the tumor periphery that progressively decreases towards the tumor core in all the tumor models. Microscale analysis revealed that NP extravasation from blood vessels increases in a time dependent manner and plateaus at 72 h post injection. Volumetric analysis and pharmacokinetic modeling of NP biodistribution in the vicinity of the blood vessels revealed that the local NP density exhibits a distance dependent spatiotemporal biodistribution which provide insights into the dynamics of NP extravasation in the tumor tissue. Our data represents a comprehensive analysis of NP biodistribution at multiple length scales in different tumor models providing unique insights into their spatiotemporal dynamics. Specifically, our results show that NPs exhibit a dynamic equilibrium with macroscale heterogeneity combined with microscale homogeneity.

Revisiting PFA-mediated tissue fixation chemistry: FixEL enables trapping of small molecules in the brain to visualize their distribution changes

Various small molecules have been used as functional probes for tissue imaging in medical diagnosis and pharmaceutical drugs for disease treatment. The spatial distribution, target selectivity, and diffusion/excretion kinetics of small molecules in structurally complicated specimens are critical for function. However, robust methods for precisely evaluating these parameters in the brain have been limited. Herein, we report a new method termed "fixation-driven chemical cross-linking of exogenous ligands (FixEL)," which traps and images exogenously administered molecules of interest (MOIs) in complex tissues. This method relies on protein-MOI interactions and chemical cross-linking of amine-tethered MOI with paraformaldehyde used for perfusion fixation. FixEL is used to obtain images of the distribution of the small molecules, which addresses selective/nonselective binding to proteins, time-dependent localization changes, and diffusion/retention kinetics of MOIs such as the scaffold of PET tracer derivatives or drug-like small molecules.

Advancements in the Use of Hydrogels for Regenerative Medicine: Properties and Biomedical Applications

Due to their particular water absorption capacity, hydrogels are the most widely used scaffolds in biomedical studies to regenerate damaged tissue. Hydrogels can be used in tissue engineering to design scaffolds for three-dimensional cell culture, providing a novel alternative to the traditional two-dimensional cell culture as hydrogels have a three-dimensional biomimetic structure. This material property is crucial in regenerative medicine, especially for the nervous system, since it is a highly complex and delicate structure. Hydrogels can move quickly within the human body without physically disturbing the environment and possess essential biocompatible properties, as well as the ability to form a mimetic scaffold in situ. Therefore, hydrogels are perfect candidates for biomedical applications. Hydrogels represent a potential alternative to regenerating tissue lost after removing a brain tumor and/or brain injuries. This reason presents them as an exciting alternative to highly complex human physiological problems, such as injuries to the central nervous system and neurodegenerative disease.

EZ Clear for simple, rapid, and robust mouse whole organ clearing

Tissue clearing for whole organ cell profiling has revolutionized biology and imaging for exploration of organs in three-dimensional space without compromising tissue architecture. But complicated, laborious procedures, or expensive equipment, as well as the use of hazardous, organic solvents prevent the widespread adoption of these methods. Here, we report a simple and rapid tissue clearing method, EZ Clear, that can clear whole adult mouse organs in 48 hr in just three simple steps. Samples stay at room temperature and remain hydrated throughout the clearing process, preserving endogenous and synthetic fluorescence, without altering sample size. After wholemount clearing and imaging, samples processed with EZ Clear can be subjected to downstream applications, such as tissue embedding and cryosectioning followed by standard histology or immunofluorescent staining without loss of fluorescence signal from endogenous or synthetic reporters. Furthermore, we demonstrate that wholemount adult mouse brains processed with EZ Clear can be successfully immunolabeled for fluorescent imaging while still retaining signal from endogenous fluorescent reporters. Overall, the simplicity, speed, and flexibility of EZ Clear make it easy to adapt and implement in diverse imaging modalities in biomedical research.

Responsive Hydrogels Based on Triggered Click Reactions for Liver Cancer

Globally, liver cancer, which is one of the major cancers worldwide, has attracted the growing attention of technological researchers for its high mortality and limited treatment options. Hydrogels are soft 3D network materials containing a large number of hydrophilic monomers. By adding moieties such as nitrobenzyl groups to the network structure of a cross-linked nanocomposite hydrogel, the click reaction improves drug-release efficiency in vivo, which improves the survival rate and prolongs the survival time of liver cancer patients. The application of a nanocomposite hydrogel drug delivery system can not only enrich the drug concentration at the tumor site for a long time but also effectively prevents the distant metastasis of residual tumor cells. At present, a large number of researches have been working toward the construction of responsive nanocomposite hydrogel drug delivery systems, but there are few comprehensive articles to systematically summarize these discoveries. Here, this systematic review summarizes the synthesis methods and related applications of nanocomposite responsive hydrogels with actions to external or internal physiological stimuli. With different physical or chemical stimuli, the structural unit rearrangement and the controlled release of drugs can be used for responsive drug delivery in different states.

Biomaterials constructed for MSC-derived extracellular vesicle loading and delivery—a promising method for tissue regeneration

Mesenchymal stem cells (MSCs) have become the preferred seed cells for tissue regeneration. Nevertheless, due to their immunogenicity and tumorigenicity, MSC transplantation remains questionable. Extracellular vesicles (EVs) derived from MSCs are becoming a promising substitute for MSCs. As a route of the MSC paracrine, EVs have a nano-sized and bilayer lipid-enclosed structure, which can guarantee the integrity of their cargoes, but EVs cannot obtain full function in vivo because of the rapid biodegradation and clearance by phagocytosis. To improve the efficacy and targeting of EVs, methods have been proposed and put into practice, especially engineered vesicles and EV-controlled release systems. In particular, EVs can be cell or tissue targeting because they have cell-specific ligands on their surfaces, but their targeting ability may be eliminated by the biodegradation of the phagocytic system during circulation. Novel application strategies have been proposed beyond direct injecting. EV carriers such as biodegradable hydrogels and other loading systems have been applied in tissue regeneration, and EV engineering is also a brand-new method for higher efficacy. In this review, we distinctively summarize EV engineering and loading system construction methods, emphasizing targeting modification methods and controlled release systems for EVs, which few literature reviews have involved.

Polyester-Based Coatings for Corrosion Protection

The article is the first review encompassing the study and the applications of polyester-based coatings for the corrosion protection of steel. The impact of corrosion and the challenges encountered thus far and the solutions encountered in industry are addressed. Then, the use of polyesters as a promising alternative to current methods, such as phosphating, chromating, galvanization, and inhibitors, are highlighted. The classifications of polyesters and the network structure determine the overall applications and performance of the polymer. The review provides new trends in green chemistry and smart and bio-based polyester-based coatings. Finally, the different applications of polyesters are covered; specifically, the use of polyesters in surface coatings and for other industrial uses is discussed.

Nanoscale fluorescence imaging of biological ultrastructure via molecular anchoring and physical expansion

Nanoscale imaging of biological samples can provide rich morphological and mechanistic information about biological functions and dysfunctions at the subcellular and molecular level. Expansion microscopy (ExM) is a recently developed nanoscale fluorescence imaging method that takes advantage of physical enlargement of biological samples. In ExM, preserved cells and tissues are embedded in a swellable hydrogel, to which the molecules and fluorescent tags in the samples are anchored. When the hydrogel swells several-fold, the effective resolution of the sample images can be improved accordingly via physical separation of the retained molecules and fluorescent tags. In this review, we focus on the early conception and development of ExM from a biochemical and materials perspective. We first examine the general workflow as well as the numerous variations of ExM developed to retain and visualize a broad range of biomolecules, such as proteins, nucleic acids, and membranous structures. We then describe a number of inherent challenges facing ExM, including those associated with expansion isotropy and labeling density, as well as the ongoing effort to address these limitations. Finally, we discuss the prospect and possibility of pushing the resolution and accuracy of ExM to the single-molecule scale and beyond.

Degradation of Hydrogels Based on Potassium and Sodium Polyacrylate by Ionic Interaction and Its Influence on Water

Hydrogels are a very useful type of polymeric material in several economic sectors, acquiring great importance due to their potential applications; however, this type of material, similarly to all polymers, is susceptible to degradation, which must be studied to improve its use. In this sense, the present work shows the degradation phenomena of commercial hydrogels based on potassium and sodium polyacrylate caused by the intrinsic content of different types of potable waters and aqueous solutions. In this way, a methodology for the analysis of this type of phenomenon is presented, facilitating the understanding of this type of degradation phenomenon. In this context, the hydrogels were characterized through swelling and FTIR to verify their performance and their structural changes. Likewise, the waters and wastewaters used for the swelling process were characterized by turbidity, pH, hardness, metals, total dissolved solids, electrical conductivity, DLS, Z-potential, and UV-vis to determine the changes generated in the types of waters caused by polymeric degradation and which are the most relevant variables in the degradation of the studied materials. The results obtained suggest a polymeric degradation reducing the swelling capacity and the useful life of the hydrogel; in addition, significant physicochemical changes such as the emergence of polymeric nanoparticles are observed in some types of analyzed waters.

Hydrogel Stamping for Rapid, Multiplexed, Point-of-Care Immunostaining of Cells and Tissues

In the era of precision oncology, multicolor fluorescence imaging has become a core technology for multiplexed molecular analysis of cellular and tissue specimens. However, conventional solution-based staining is labor-intensive and time-consuming and requires considerable expertise to yield optimal results, which creates difficulties for employing this technology in resource-limited settings. Here, we report a new immunostaining method based on hydrogel stamping, which is simple, fast, easy to use, and reproducible. We showed that a hydrophilic hydrogel stamp could effectively transfer fluorescent antibodies to targets and withdraw an excess solution when the reaction is completed, obviating the need for extra washing. This unique property allows for quality immunostaining in 5 min for cells using one-eighth of antibody consumption compared to the conventional solution-based method. Furthermore, we implemented fluorescence quenching and immunocycling with hydrogel staining for multiplexed analysis of 9 protein markers at a single cell level. Finally, we applied the immunocycling method to human breast cancer tissue samples and showed quality immunostaining over a large area (∼2 cm²) in 30 min for molecular subtyping of breast cancer. The hydrogel immunostaining could open new opportunities for rapid, automated, and multiplexed profiling in compact point-of-care systems for molecular cancer diagnosis.

Expansion microscopy with ninefold swelling (NIFS) hydrogel permits cellular ultrastructure imaging on conventional microscope

Superresolution microscopy enables probing of cellular ultrastructures. However, its widespread applications are limited by the need for expensive machinery, specific hardware, and sophisticated data processing. Expansion microscopy (ExM) improves the resolution of conventional microscopy by physically expanding biological specimens before imaging and currently provides ~70-nm resolution, which still lags behind that of modern superresolution microscopy (~30 nm). Here, we demonstrate a ninefold swelling (NIFS) hydrogel, that can reduce ExM resolution to 31 nm when using regular traditional microscopy. We also design a detachable chip that integrates all the experimental operations to facilitate the maximal reproducibility of this high-resolution imaging technology. We demonstrate this technique on the superimaging of nuclear pore complex and clathrin-coated pits, whose structures can hardly be resolved by conventional microscopy. The method presented here offers a universal platform with superresolution imaging to unveil cellular ultrastructural details using standard conventional laboratory microscopes.

Neuroanatomical Basis for the Orexinergic Modulation of Anesthesia Arousal and Pain Control

Hypothalamic orexin (hypocretin) neurons play crucial roles in arousal control. Their involvement in anesthesia and analgesia remains to be better understood. In order to enhance our view on the neuroanatomy, we systematically mapped the projections of orexin neurons with confocal microscope and light sheet microscope. We specifically expressed optogenetic opsins tagged with fluorescence markers in orexin neurons through adeno-associated viral infection in the mouse brain. The imaging results revealed fine details and novel features of the orexin projections throughout the brain, particularly related to the nuclei regulating arousal and pain. We then optogenetically activated orexin neurons in the lateral hypothalamus to study the effects on anesthesia-related behaviors. cFos staining showed that optogenetic stimulation can activate orexin neurons in the ChR2-mCherry group, but not the control mCherry group (62.86 ± 3.923% vs. 7.9 ± 2.072%; P < 0.0001). In behavior assays, optogenetic stimulation in the ChR2-mCherry group consistently elicited robust arousal from light isoflurane anesthesia (9.429 ± 3.804 s vs. 238.2 ± 17.42 s; P < 0.0001), shortened the emergence time after deep isoflurane anesthesia (109.5 ± 13.59 s vs. 213.8 ± 21.77 s; P = 0.0023), and increased the paw withdrawal latency in a hotplate test (11.45 ± 1.185 s vs. 8.767 ± 0.7775; P = 0.0317). The structural details of orexin fibers established the neuroanatomic basis for studying the role of orexin in anesthesia and analgesia.

Cell-based biocomposite engineering directed by polymers

Biological cells such as bacterial, fungal, and mammalian cells always exploit sophisticated chemistries and exquisite micro- and nano-structures to execute life activities, providing numerous templates for engineering bioactive and biomorphic materials, devices, and systems. To transform biological cells into functional biocomposites, polymer-directed cell surface engineering and intracellular functionalization have been developed over the past two decades. Polymeric materials can be easily adopted by various cells through polymer grafting or in situ hydrogelation and can successfully bridge cells with other functional materials as interfacial layers, thus achieving the manufacture of advanced biocomposites through bioaugmentation of living cells and transformation of cells into templated materials. This review article summarizes the recent progress in the design and construction of cell-based biocomposites by polymer-directed strategies. Furthermore, the applications of cell-based biocomposites in broad fields such as cell research, biomedicine, and bioenergy are discussed. Last, we provide personal perspectives on challenges and future trends in this interdisciplinary area.

Optical tissue clearing associated with 3D imaging: application in preclinical and clinical studies

Understanding the inner morphology of intact tissues is one of the most competitive challenges in modern biology. Since the beginning of the twentieth century, optical tissue clearing (OTC) has provided solutions for volumetric imaging, allowing the microscopic visualization of thick sections of tissue, organoids, up to whole organs and organisms (for example, mouse or rat). Recently, tissue clearing has also been introduced in clinical settings to achieve a more accurate diagnosis with the support of 3D imaging. This review aims to give an overview of the most recent developments in OTC and 3D imaging and to illustrate their role in the field of medical diagnosis, with a specific focus on clinical applications.

High-throughput Genetically Modified Animal Experiments Achieved by Next-generation Mammalian Genetics

Animal models are essential tools for modern scientists to conduct biological experiments and investigate their hypotheses in vivo. However, for the past decade, raising the throughput of such animal experiments has been a great challenge. Conventionally, in vivo high-throughput assay was achieved through large-scale mutagen-driven forward genetic screening, which took years to find causal genes. In contrast, reverse genetics accelerated the causal gene identification process, but its throughput was also limited by 2 barriers, that is, the genome modification step and the time-consuming crossing step. Defined as genetics without crossing, next-generation genetics is able to produce gene-modified animals that can be analyzed at the founder generation (F0). This method is or can be accomplished through recent technological advances in gene editing and virus-based efficient gene modifications. Notably, next-generation genetics has accelerated the process of cross-species studies, and it will be a useful technique during animal experiments as it can provide genetic perturbation at an individual level without crossing. In this review, we begin by introducing the history of animal-based high-throughput analysis, with a specific focus on chronobiology. We then describe ways that gene modification efficiency during animal experiments was enhanced and why crossing remained a barrier to reaching higher efficiency. Moreover, we mention the Triple CRISPR as a critical technique for achieving next-generation genetics. Finally, we discuss the potential applications and limitations of next-generation mammalian genetics.

TISSUE CLEARING

Tissue clearing of gross anatomical samples was first described over a century ago and has only recently found widespread use in the field of microscopy. This renaissance has been driven by the application of modern knowledge of optical physics and chemical engineering to the development of robust and reproducible clearing techniques, the arrival of new microscopes that can image large samples at cellular resolution and computing infrastructure able to store and analyze large data volumes. Many biological relationships between structure and function require investigation in three dimensions and tissue clearing therefore has the potential to enable broad discoveries in the biological sciences. Unfortunately, the current literature is complex and could confuse researchers looking to begin a clearing project. The goal of this Primer is to outline a modular approach to tissue clearing that allows a novice researcher to develop a customized clearing pipeline tailored to their tissue of interest. Further, the Primer outlines the required imaging and computational infrastructure needed to perform tissue clearing at scale, gives an overview of current applications, discusses limitations and provides an outlook on future advances in the field.

CLARITY and Light-Sheet microscopy sample preparation in application to human cerebral organoids

Cerebral organoids are three-dimensional cell-culture systems that represent a unique experimental model reconstructing early events of human neurogenesis in vitro in health and various pathologies. The most commonly used approach to studying the morphological parameters of organoids is immunohistochemical analysis; therefore, the three-dimensional cytoarchitecture of organoids, such as neural networks or asymmetric internal organization, is difficult to reconstruct using routine approaches. Immunohistochemical analysis of biological objects is a universal method in biological research. One of the key stages of this method is the production of cryo- or paraffin serial sections of samples, which is a very laborious and time-consuming process. In addition, slices represent only a tiny part of the object under study; three-dimensional reconstruction from the obtained serial images is an extremely complex process and often requires expensive special programs for image processing. Unfortunately, staining and microscopic examination of samples are difficult due to their low permeability and a high level of autofluorescence. Tissue cleaning technologies combined with Light-Sheet microscopy allows these challenges to be overcome. CLARITY is one of the tissue preparation techniques that makes it possible to obtain opaque biological objects transparent while maintaining the integrity of their internal structures. This method is based on a special sample preparation, during which lipids are removed from cells and replaced with hydrogel compounds such as acrylamide, while proteins and nucleic acids remain intact. CLARITY provides researchers with a unique opportunity to study three-dimensional biological structures while preserving their internal organization, including whole animals or embryos, individual organs and artificially grown organoids, in particular cerebral organoids. This protocol summarizes an optimization of CLARITY conditions for human brain organoids and the preparation of Light-Sheet microscopy samples.

Continuous subcellular resolution three-dimensional imaging on intact macaque brain

To decipher the organizational logic of complex brain circuits, it is important to chart long-distance pathways while preserving micron-level accuracy of local network. However, mapping the neuronal projections with individual-axon resolution in the large and complex primate brain is still challenging. Herein, we describe a highly efficient pipeline for three-dimensional mapping of the entire macaque brain with subcellular resolution. The pipeline includes a novel poly-N-acryloyl glycinamide (PNAGA)-based embedding method for long-term structure and fluorescence preservation, high-resolution and rapid whole-brain optical imaging, and image post-processing. The cytoarchitectonic information of the entire macaque brain was acquired with a voxel size of 0.32 μm × 0.32 μm × 10 μm, showing its anatomical structure with cell distribution, density, and shape. Furthermore, thanks to viral labeling, individual long-distance projection axons from the frontal cortex were for the first time reconstructed across the entire brain hemisphere with a voxel size of 0.65 μm × 0.65 μm × 3 μm. Our results show that individual cortical axons originating from the prefrontal cortex simultaneously target multiple brain regions, including the visual cortex, striatum, thalamus, and midbrain. This pipeline provides an efficient method for cellular and circuitry investigation of the whole macaque brain with individual-axon resolution, and can shed light on brain function and disorders.

Hydrogels for Treatment of Oral and Maxillofacial Diseases: Current Research, Challenge, and Future Directions

Oral and maxillofacial diseases such as infection and trauma often involve various organs and tissues, resulting in structural defects, dysfunctions and/or adverse effects on facial appearance. Hydrogels have been applied...

Hydrophobic and Hydrogel-Based Methods for Passive Tissue Clearing

Optical tissue clearing enables the precise imaging of cellular and subcellular structures in whole organs and tissues without the need for physical tissue sectioning. By combining tissue clearing with confocal or lightsheet microscopy, 3D images can be generated of entire specimens for visualization and large-scale data analysis. Here we demonstrate two different passive tissue clearing techniques that are compatible with immunofluorescent staining and lightsheet microscopy: PACT, an aqueous hydrogel-based clearing method, and iDISCO+, an organic solvent-based clearing method.

Portable fluid circuit device containing printed silicone microvessels as a training aid for arterial microanastomosis

Anastomosis of the microvessels requires high-level skills and extensive basic training. This study was performed to introduce and evaluate an inexpensive laboratory device as a training aid. Micro-tubes of 0.8 mm inner diameter and 0.5/0.8 mm wall thickness mimicking human vein/artery were printed from a silicon-containing hydrogel using three-dimensional printing technology. The hydrogel components are optimized to render the printed tubes biomechanical features resembling the blood vessels of a living organism. These artificial vessels were connected to a pump for fluid flow, simulating the blood circulation. Forty medical interns were assigned to two equal groups. The 20 interns in group A practiced anastomosis using the training aid for a total of 10 hours over 5 days. The 20 interns in group B practiced anastomosis using the traditional gum pieces and silicone tubes. Then, all interns performed anastomosis on rat carotid arteries, and their performance was scored by a team of five experienced maxillofacial surgeons. The average success score and time required for anastomosis were compared between the two groups. The mean success score of group A was significantly higher than that of group B (0.83 ± 0.12 vs 0.64 ± 0.10, P < 0.001). The mean anastomosis time of group A was significantly shorter than that of group B (10.2 ± 1.1 vs 17.2 ± 1.4 minutes, P < 0.001). This training device for vessel microanastomosis is an inexpensive, practical, and effective tool for use in laboratories and also reduces the use of animals.

Towards organism-level systems biology by next-generation genetics and whole-organ cell profiling

The system-level identification and analysis of molecular and cellular networks in mammals can be accelerated by "next-generation" genetics, which is defined as genetics that can achieve desired genetic makeup in a single generation without any animal crossing. We recently established a highly efficient procedure for producing knock-out (KO) mice using the "Triple-CRISPR" method, which targets a single gene by triple gRNAs in the CRISPR/Cas9 system. This procedure achieved an almost perfect KO efficiency (96-100%). We also established a highly efficient procedure, the "ES-mouse" method, for producing knock-in (KI) mice within a single generation. In this method, ES cells were treated with three inhibitors to keep their potency and then injected into 8-cell-stage embryos. These procedures dramatically shortened the time required to produce KO or KI mice from years down to about 3 months. The produced KO and KI mice can also be systematically profiled at a single-cell resolution by the "whole-organ cell profiling," which was realized by tissue-clearing methods, such as CUBIC, and an advanced light-sheet microscopy. The review describes the establishment and application of these technologies above in analyzing the three states (NREM sleep, REM sleep, and awake) of mammalian brains. It also discusses the role of calcium and muscarinic receptors in these states as well as the current challenges and future opportunities in the next-generation mammalian genetics and whole-organ cell profiling for organism-level systems biology.

Tutorial: methods for three-dimensional visualization of archival tissue material

Analysis of three-dimensional patient specimens is gaining increasing relevance for understanding the principles of tissue structure as well as the biology and mechanisms underlying disease. New technologies are improving our ability to visualize large volume of tissues with subcellular resolution. One resource often overlooked is archival tissue maintained for decades in hospitals and research archives around the world. Accessing the wealth of information stored within these samples requires the use of appropriate methods. This tutorial introduces the range of sample preparation and microscopy approaches available for three-dimensional visualization of archival tissue. We summarize key aspects of the relevant techniques and common issues encountered when using archival tissue, including registration and antibody penetration. We also discuss analysis pipelines required to process, visualize and analyze the data and criteria to guide decision-making. The methods outlined in this tutorial provide an important and sustainable avenue for validating three-dimensional tissue organization and mechanisms of disease.

Tissue clearing and 3D imaging - putting immune cells into context

A better understanding of cell-cell and cell-niche interactions is crucial to comprehend the complexity of inflammatory or pathophysiological scenarios such as tissue damage during viral infections, the tumour microenvironment and neuroinflammation. Optical clearing and 3D volumetric imaging of large tissue pieces or whole organs is a rapidly developing methodology that holds great promise for the in-depth study of cells in their natural surroundings. These methods have mostly been applied to image structural components such as endothelial cells and neuronal architecture. Recent work now highlights the possibility of studying immune cells in detail within their respective immune niches. This Review summarizes recent developments in tissue clearing methods and 3D imaging, with a focus on the localization and quantification of immune cells. We first provide background to the optical challenges involved and their solutions before discussing published protocols for tissue clearing, the limitations of 3D imaging of immune cells and image analysis. Furthermore, we highlight possible applications for tissue clearing and propose future developments for the analysis of immune cells within homeostatic or inflammatory immune niches.

Expansion microscopy: A powerful nanoscale imaging tool for neuroscientists

One of the biggest unsolved questions in neuroscience is how molecules and neuronal circuitry create behaviors, and how their misregulation or dysfunction results in neurological disease. Light microscopy is a vital tool for the study of neural molecules and circuits. However, the fundamental optical diffraction limit precludes the use of conventional light microscopy for sufficient characterization of critical signaling compartments and nanoscopic organizations of synapse-associated molecules. We have witnessed rapid development of super-resolution microscopy methods that circumvent the resolution limit by controlling the number of emitting molecules in specific imaging volumes and allow highly resolved imaging in the 10-100 nm range. Most recently, Expansion Microscopy (ExM) emerged as an alternative solution to overcome the diffraction limit by physically magnifying biological specimens, including nervous systems. Here, we discuss how ExM works in general and currently available ExM methods. We then review ExM imaging in a wide range of nervous systems, including Caenorhabditis elegans, Drosophila, zebrafish, mouse, and human, and their applications to synaptic imaging, neuronal tracing, and the study of neurological disease. Finally, we provide our prospects for expansion microscopy as a powerful nanoscale imaging tool in the neurosciences.

A Gelatin-Hyaluronic Acid Double Cross-Linked Hydrogel for Regulating the Growth and Dual Dimensional Cartilage Differentiation of Bone Marrow Mesenchymal Stem Cells

Owing to its unique physiochemical properties similar to the extracellular matrix (ECM), three-dimensional (3D) crosslinked hydrogels are widely studied materials for tissue engineering. In this study, to mimic the ECM microenvironment, a two-step covalent cross-linking with hyaluronic acid and gelatin was performed to form an interpenetrating polymer network structure. Gelatin as the first network greatly improved the mechanical strength of the hydrogels, while a hyaluronic acid network as the second network improved the tenacity and biological activity. Compared with a single network hydrogel, the interpenetrating hydrogel system can further regulate the mechanical properties of the hydrogel by adjusting the ratio of the two components, thereby changing the proliferation, activity, and direction of cartilage differentiation of bone marrow mesenchymal stem cells (BMSCs). Not only that, with two culture methods for BMSCs on the surface and 3D wrapped in the double cross-linked hydrogels, they exhibited their potential to induce BMSCs to cartilage differentiation under the condition of 3D encapsulation of BMSCs and contact with BMSCs on its surface. As a scaffold material for cartilage tissue engineering, this double cross-linked hydrogel demonstrated its high feasibility and applicability in delivering BMSCs in vivo and repairing defects.

CUBIC-Cloud provides an integrative computational framework toward community-driven whole-mouse-brain mapping

Recent advancements in tissue clearing technologies have offered unparalleled opportunities for researchers to explore the whole mouse brain at cellular resolution. With the expansion of this experimental technique, however, a scalable and easy-to-use computational tool is in demand to effectively analyze and integrate whole-brain mapping datasets. To that end, here we present CUBIC-Cloud, a cloud-based framework to quantify, visualize, and integrate mouse brain data. CUBIC-Cloud is a fully automated system where users can upload their whole-brain data, run analyses, and publish the results. We demonstrate the generality of CUBIC-Cloud by a variety of applications. First, we investigated the brain-wide distribution of five cell types. Second, we quantified Aβ plaque deposition in Alzheimer's disease model mouse brains. Third, we reconstructed a neuronal activity profile under LPS-induced inflammation by c-Fos immunostaining. Last, we show brain-wide connectivity mapping by pseudotyped rabies virus. Together, CUBIC-Cloud provides an integrative platform to advance scalable and collaborative whole-brain mapping.

Super-resolution label-free volumetric vibrational imaging

Innovations in high-resolution optical imaging have allowed visualization of nanoscale biological structures and connections. However, super-resolution fluorescence techniques, including both optics-oriented and sample-expansion based, are limited in quantification and throughput especially in tissues from photobleaching or quenching of the fluorophores, and low-efficiency or non-uniform delivery of the probes. Here, we report a general sample-expansion vibrational imaging strategy, termed VISTA, for scalable label-free high-resolution interrogations of protein-rich biological structures with resolution down to 78 nm. VISTA achieves decent three-dimensional image quality through optimal retention of endogenous proteins, isotropic sample expansion, and deprivation of scattering lipids. Free from probe-labeling associated issues, VISTA offers unbiased and high-throughput tissue investigations. With correlative VISTA and immunofluorescence, we further validated the imaging specificity of VISTA and trained an image-segmentation model for label-free multi-component and volumetric prediction of nucleus, blood vessels, neuronal cells and dendrites in complex mouse brain tissues. VISTA could hence open new avenues for versatile biomedical studies.

Perspective: Extending the Utility of Three-Dimensional Organoids by Tissue Clearing Technologies

An organoid, a self-organizing organ-like tissue developed from stem cells, can exhibit a miniaturized three-dimensional (3D) structure and part of the physiological functions of the original organ. Due to the reproducibility of tissue complexity and ease of handling, organoids have replaced real organs and animals for a variety of uses, such as investigations of the mechanisms of organogenesis and disease onset, and screening of drug effects and/or toxicity. The recent advent of tissue clearing and 3D imaging techniques have great potential contributions to organoid studies by allowing the collection and analysis of 3D images of whole organoids with a reasonable throughput and thus can expand the means of examining the 3D architecture, cellular components, and variability among organoids. Genetic and histological cell-labeling methods, together with organoid clearing, also allow visualization of critical structures and cellular components within organoids. The collected 3D data may enable image analysis to quantitatively assess structures within organoids and sensitively/effectively detect abnormalities caused by perturbations. These capabilities of tissue/organoid clearing and 3D imaging techniques not only extend the utility of organoids in basic biology but can also be applied for quality control of clinical organoid production and large-scale drug screening.

Features of hippocampal astrocytic domains and their spatial relation to excitatory and inhibitory neurons

The mounting evidence for the involvement of astrocytes in neuronal circuits function and behavior stands in stark contrast to the lack of detailed anatomical description of these cells and the neurons in their domains. To fill this void, we imaged >30,000 astrocytes in hippocampi made transparent by CLARITY, and determined the elaborate structure, distribution, and neuronal content of astrocytic domains. First, we characterized the spatial distribution of >19,000 astrocytes across CA1 lamina, and analyzed the morphology of thousands of reconstructed domains. We then determined the excitatory somatic content of CA1 astrocytes, and measured the distance between inhibitory neuronal somata to the nearest astrocyte soma. We find that on average, there are almost 14 pyramidal neurons per domain in the CA1, increasing toward the pyramidal layer midline, compared to only five excitatory neurons per domain in the amygdala. Finally, we discovered that somatostatin neurons are found in close proximity to astrocytes, compared to parvalbumin and VIP inhibitory neurons. This work provides a comprehensive large-scale quantitative foundation for studying neuron-astrocyte interactions.

It's clearly the heart! Optical transparency, cardiac tissue imaging, and computer modelling

Recent developments in clearing and microscopy enable 3D imaging with cellular resolution up to the whole organ level. These methods have been used extensively in neurobiology, but their uptake in other fields has been much more limited. Application of this approach to the human heart and effective use of the data acquired present challenges of scale and complexity. Four interlinked issues need to be addressed: 1) efficient clearing and labelling of heart tissue, 2) fast microscopic imaging of human-scale samples, 3) handling and processing of multi-terabyte 3D images, and 4) extraction of structural information in computationally tractable structure-based models of cardiac function. Preliminary studies show that each of these requirements can be achieved with the appropriate application and development of existing technologies.

Tutorial: practical considerations for tissue clearing and imaging

Tissue clearing has become a powerful technique for studying anatomy and morphology at scales ranging from entire organisms to subcellular features. With the recent proliferation of tissue-clearing methods and imaging options, it can be challenging to determine the best clearing protocol for a particular tissue and experimental question. The fact that so many clearing protocols exist suggests there is no one-size-fits-all approach to tissue clearing and imaging. Even in cases where a basic level of clearing has been achieved, there are many factors to consider, including signal retention, staining (labeling), uniformity of transparency, image acquisition and analysis. Despite reviews citing features of clearing protocols, it is often unknown a priori whether a protocol will work for a given experiment, and thus some optimization is required by the end user. In addition, the capabilities of available imaging setups often dictate how the sample needs to be prepared. After imaging, careful evaluation of volumetric image data is required for each combination of clearing protocol, tissue type, biological marker, imaging modality and biological question. Rather than providing a direct comparison of the many clearing methods and applications available, in this tutorial we address common pitfalls and provide guidelines for designing, optimizing and imaging in a successful tissue-clearing experiment with a focus on light-sheet fluorescence microscopy (LSFM).

Biotherapeutic-loaded injectable hydrogels as a synergistic strategy to support myocardial repair after myocardial infarction

Myocardial infarction (MI) has been considered as the leading cause of cardiovascular-related deaths worldwide. Although traditional therapeutic agents including various bioactive species such as growth factors, stem cells, and nucleic acids have demonstrated somewhat usefulness for the restoration of cardiac functions, the therapeutic efficiency remains unsatisfactory most likely due to the off-target-associated side effects and low localized retention of the used therapeutic agents in the infarcted myocardium, which constitutes a substantial barrier for the effective treatment of MI. Injectable hydrogels are regarded as a minimally invasive technology that can overcome the clinical and surgical limitations of traditional stenting by a modulated sol-gel transition and localized transport of a variety of encapsulated cargoes, leading to enhanced therapeutic efficiency and improved patient comfort and compliance. However, the design of injectable hydrogels for myocardial repair and the mechanism of action of bioactive substance-loaded hydrogels for MI repair remain unclear. To elucidate these points, we summarized the recent progresses made on the use of injectable hydrogels for encapsulation of various therapeutic substances for MI treatment with an emphasis on the mechanism of action of hydrogel systems for myocardial repair. Specifically, the pathogenesis of MI and the rational design of injectable hydrogels for myocardial repair were presented. Next, the mechanisms of various biotherapeutic substance-loaded injectable hydrogels for myocardial repair was discussed. Finally, the potential challenges and future prospects for the use of injectable hydrogels for MI treatment were proposed for the purpose of drawing theoretical guidance on the development of novel therapeutic strategies for efficient treatment of MI.

A Versatile Tiling Light Sheet Microscope for Imaging of Cleared Tissues

We present a tiling light sheet microscope compatible with all tissue clearing methods for rapid multicolor 3D imaging of cleared tissues with micron-scale (4 × 4 × 10 μm³) to submicron-scale (0.3 × 0.3 × 1 μm³) spatial resolution. The resolving ability is improved to sub-100 nm (70 × 70 × 200 nm³) via tissue expansion. The microscope uses tiling light sheets to achieve higher spatial resolution and better optical sectioning ability than conventional light sheet microscopes. The illumination light is phase modulated to adjust the position and intensity profile of the light sheet based on the desired spatial resolution and imaging speed and to keep the microscope aligned. The ability of the microscope to align via phase modulation alone also ensures its accuracy for multicolor 3D imaging and makes the microscope reliable and easy to operate. Here we describe the working principle and design of the microscope. We demonstrate its utility by imaging various cleared tissues.

[Development in Tissue Clearing Technology and Its Application in Neurodegenerative Diseases]

Modern tissue clearing techniques have made it possible to have high-resolution imaging of cell populations and three-dimensional reconstruction of tissue structures, and we are able to obtain more complete three-dimensional brain structures and spatial connections between the various components of brain tissues through tissue clearing techniques. Over the past decade, scientists have developed and improved a number of tissue clearing techniques that are now widely used in neuroscience research, allowing us to extract important information from complex neural networks. Moreover, tissue clearing technology also provides research tools for the stem cell therapy and neurogeneration of neurodegenerative diseases. In this paper, we reviewed the major types of existing tissue clearing techniques and their respective strengths and weaknesses. We summarized the application of these techniques in neurodegenerative disease research and their unique merits. In addition, we explored the development requirements of tissue clearing technology, improvements in the supporting equipment, and its potential to be used as research tools for stem cell therapy and regenerative medicine in the future.

Ferrocene-functionalized hybrid hydrogel dressing with high-adhesion for combating biofilm

Bacterial infection is a common phenomenon in the process of postoperative wound healing. In severe cases, it may even lead to life-threatening, which brings a heavy burden to the clinical treatment and causes huge losses to the society and economy. As one of the most commonly applied medical materials for wound treatment, hydrogel dressings are mainly used to cover and protect wounds and provide a favorable environment to facilitate wound healing. In this work, we developed an antibacterial hydrogel dressing (Fc-PAAM) with high adhesion, which is consisted of polyacrylamide (PAM) hydrogel framework and polyacrylic acid-functionalized (PAA) with ferrocene (Fc). Morphology, adhesion and pressure resistance of PAAM hydrogel were confirmed by using scanning electron microscope (SEM) and universal testing machine, and Fc decoration in the hydrogel network was well demonstrated by using Fourier transform infrared spectroscopy (FT-IR). Ultraviolet-visible spectroscopy (UV-vis) displayed that the Fc-PAAM hydrogel had excellent peroxidase-like activity as well. It not only exhibited prominent antimicrobial activity against Gram (+/-) bacteria, but also performed high efficiency in preventing the formation of biofilms. In addition, in vivo experiments indicated that this adhesive dressing could significantly prevent bacterial infections. Compared with other clinical treatment methods, this kind of hydrogel is not easy to cause bacterial resistance, and the used raw materials are easy to obtain and low in price, which can amplify the antibacterial properties of H₂O₂ and provide a new opportunity for the treatment of clinical bacterial infections.

Advanced imaging and labelling methods to decipher brain cell organization and function

The brain is arguably the most complex organ. The branched and extended morphology of nerve cells, their subcellular complexity, the multiplicity of brain cell types as well as their intricate connectivity and the scattering properties of brain tissue present formidable challenges to the understanding of brain function. Neuroscientists have often been at the forefront of technological and methodological developments to overcome these hurdles to visualize, quantify and modify cell and network properties. Over the last few decades, the development of advanced imaging methods has revolutionized our approach to explore the brain. Super-resolution microscopy and tissue imaging approaches have recently exploded. These instrumentation-based innovations have occurred in parallel with the development of new molecular approaches to label protein targets, to evolve new biosensors and to target them to appropriate cell types or subcellular compartments. We review the latest developments for labelling and functionalizing proteins with small localization and functionalized reporters. We present how these molecular tools are combined with the development of a wide variety of imaging methods that break either the diffraction barrier or the tissue penetration depth limits. We put these developments in perspective to emphasize how they will enable step changes in our understanding of the brain.

A guidebook for DISCO tissue clearing

Histological analysis of biological tissues by mechanical sectioning is significantly time-consuming and error-prone due to loss of important information during sample slicing. In the recent years, the development of tissue clearing methods overcame several of these limitations and allowed exploring intact biological specimens by rendering tissues transparent and subsequently imaging them by laser scanning fluorescence microscopy. In this review, we provide a guide for scientists who would like to perform a clearing protocol from scratch without any prior knowledge, with an emphasis on DISCO clearing protocols, which have been widely used not only due to their robustness, but also owing to their relatively straightforward application. We discuss diverse tissue-clearing options and propose solutions for several possible pitfalls. Moreover, after surveying more than 30 researchers that employ tissue clearing techniques in their laboratories, we compiled the most frequently encountered issues and propose solutions. Overall, this review offers an informative and detailed guide through the growing literature of tissue clearing and can help with finding the easiest way for hands-on implementation.

Peptide-Protein Interactions: From Drug Design to Supramolecular Biomaterials

The self-recognition and self-assembly of biomolecules are spontaneous processes that occur in Nature and allow the formation of ordered structures, at the nanoscale or even at the macroscale, under thermodynamic and kinetic equilibrium as a consequence of specific and local interactions. In particular, peptides and peptidomimetics play an elected role, as they may allow a rational approach to elucidate biological mechanisms to develop new drugs, biomaterials, catalysts, or semiconductors. The forces that rule self-recognition and self-assembly processes are weak interactions, such as hydrogen bonding, electrostatic attractions, and van der Waals forces, and they underlie the formation of the secondary structure (e.g., α-helix, β-sheet, polyproline II helix), which plays a key role in all biological processes. Here, we present recent and significant examples whereby design was successfully applied to attain the desired structural motifs toward function. These studies are important to understand the main interactions ruling the biological processes and the onset of many pathologies. The types of secondary structure adopted by peptides during self-assembly have a fundamental importance not only on the type of nano- or macro-structure formed but also on the properties of biomaterials, such as the types of interaction, encapsulation, non-covalent interaction, or covalent interaction, which are ultimately useful for applications in drug delivery.

Current Status of Tissue Clearing and the Path Forward in Neuroscience

Due to the complexity and limited availability of human brain tissues, for decades, pathologists have sought to maximize information gained from individual samples, based on which (patho)physiological processes could be inferred. Recently, new understandings of chemical and physical properties of biological tissues and multiple chemical profiling have given rise to the development of scalable tissue clearing methods allowing superior optical clearing of across-the-scale samples. In the past decade, tissue clearing techniques, molecular labeling methods, advanced laser scanning microscopes, and data visualization and analysis have become commonplace. Combined, they have made 3D visualization of brain tissues with unprecedented resolution and depth widely accessible. To facilitate further advancements and applications, here we provide a critical appraisal of these techniques. We propose a classification system of current tissue clearing and expansion methods that allows users to judge the applicability of individual ones to their questions, followed by a review of the current progress in molecular labeling, optical imaging, and data processing to demonstrate the whole 3D imaging pipeline based on tissue clearing and downstream techniques for visualizing the brain. We also raise the path forward of tissue-clearing-based imaging technology, that is, integrating with state-of-the-art techniques, such as multiplexing protein imaging, in situ signal amplification, RNA detection and sequencing, super-resolution imaging techniques, multiomics studies, and deep learning, for drawing the complete atlas of the human brain and building a 3D pathology platform for central nervous system disorders.