Molecular Labeling Research Articles

Tissue clearing technique: Recent progress and biomedical applications.

Organisms are inherently three dimensional, thus comprehensive understanding of the complicated biological system requires analysis of organs or even whole bodies in the context of three dimensions. However, this is a tremendous task since the biological specimens are naturally opaque, a major obstacle in whole-body and whole-organ imaging. Tissue clearing technique provides a prospective solution and has become a powerful tool for three-dimensional imaging and quantification of organisms. Tissue clearing technique aims to make tissue transparent by minimizing light scattering and light absorption, thus allowing deep imaging of large volume samples. When combined with diverse molecular labeling methods and high-throughput optical sectioning microscopes, tissue clearing technique enables whole-body and whole-organ imaging at cellular or subcellular resolution, providing detailed and comprehensive information about the intact biological systems. Here, we give an overview of recent progress and biomedical applications of tissue clearing technique. We introduce the mechanisms and basic principles of tissue clearing, and summarize the current tissue clearing methods. Moreover, the available imaging techniques and software packages for data processing are also presented. Finally, we introduce the recent advances in applications of tissue clearing in biomedical fields. Tissue clearing contributes to the investigation of structure-function relationships in intact mammalian organs, and opens new avenues for cellular and molecular mapping of intact human organs. We hope this review contributes to a better understanding of tissue clearing technique and can help researchers to select the best-suited clearing protocol for their experiments.

High-Fidelity Determination and Tracing of Small Extracellular Vesicle Cargoes.

Direct tracing of small extracellular vesicle (sEV) cargoes holds unprecedented importance for elucidating the mechanisms involved in intercellular communication. However, high-fidelity determination of sEVs' molecular cargoes in situ has yet to be achieved due to the difficulty in transporting molecular probes into intact sEVs. Herein, a fLuorescent Intracellular-Guided Hairpin-Tetrahedron (fLIGHT) nanoprobe is described for direct visualization of sEV microRNAs in situ. Integrating the advantages of nondestructive sEV penetration via DNA origami and single-nucleotide discrimination as well as wash-free fluorescence readout using a hairpin probe, the proposed approach enables high-fidelity fluorescence visualization of sEVs' microRNA without RNA extraction or leakage, demonstrating the potential of on-site tracing of sEV cargoes. This strategy opens an avenue to establishing universal molecular detection and labeling platforms that can facilitate both sEV-derived fundamental biological studies and molecular diagnostics.

Functions and applications of metallic and metallic oxide nanoparticles in orthopedic implants and scaffolds.

Bone defects and diseases are devastating, and can lead to severe functional deficits or even permanent disability. Nevertheless, orthopedic implants and scaffolds can facilitate the growth of incipient bone and help us to treat bone defects and diseases. Currently, a wide range of biomaterials with distinct biocompatibility, biodegradability, porosity, and mechanical strength is used in bone-related research. However, most orthopedic implants and scaffolds have certain limitations and diverse complications, such as limited corrosion resistance, low cell proliferation, and bacterial adhesion. With recent advancements in materials science and nanotechnology, metallic and metallic oxide nanoparticles have become the subject of significant interest as they offer an ample variety of options to resolve the existing problems in the orthopedic industry. More importantly, these nanoparticles possess unique physicochemical and mechanical properties not found in conventional materials, and can be incorporated into orthopedic implants and scaffolds to enhance their antimicrobial ability, bioactive molecular delivery, mechanical strength, osteointegration, and cell labeling and imaging. However, many metallic and metallic oxide nanoparticles can also be toxic to nearby cells and tissues. This review article will discuss the applications and functions of metallic and metallic oxide nanoparticles in orthopedic implants and bone tissue engineering.

Microfabricated Nano-Gap Tunneling Current Zika Virus Sensors With Single Virus Detection Capabilities

Electron tunneling through thin ( ~ 1-50 nm), insulating materials can provide information regarding their band structure, density of states, surface and bulk defect densities and their energy levels and distributions. While electron tunneling has been used in thin inorganic insulating materials for nearly 7 decades, its applications in organic and biological materials, with exceptions of deoxyribonucleic acid and a few other materials, are not extensively explored. Here we report room temperature electron tunneling studies to differentiate between aptamers designed to attach to the capsid proteins on Zika viruses and the aptamer-Zika complexes. We show that the electron tunneling induced by the current versus voltage (I-V) measurements through these materials contain information that enable identification of the Zika virus without any need for DNA sequencing or additional molecular labels. The electron tunneling measurements were carried out using a conducting atomic force microscope, a home-made vertical tunneling junction and an electromigration-induced nanogap in a microfabricated 1 μm -wide gold line on silicon nitride bridges. The current through aptamers and aptamer-Zika complexes all have a threshold voltage just before the exponential increase in the junction current. Below this voltage, the leakage currents are different for the aptamer and aptamer-Zika samples. The tunnel nanogap device is suitable for detecting viruses that are nanometer-scale biomaterials.

The content of yellow pigments in durum wheat (Titicum durum Desf.) grains: biosynthesis, genetic control, marker selection

Зерно с высоким содержанием каротиноидных пигментов ценится за ярко-желтый цвет пасты, производимой из него, и провитаминную (витамин А) и антиоксидантную активность пигментов. Цель настоя- щего обзора – обобщение современных знаний о биосинтезе и генетическом контроле накопления пигментов в зерне твердой пшеницы и оценка основных результатов исследований и селекции за последние двадцать лет за рубежом и в России. Признак «концентрация каротиноидных пигментов в зерне» (Ypc) относится к раз- ряду количественных. Тем не менее превалирование сильных аддитивных эффектов генов и высокая насле- дуемость способствовали значительному прогрессу в селекции по этому признаку. Методами молекулярного маркирования локусов количественных признаков (QTL), контролирующих синтез каротиноидных пигментов и значения индекса желтизны (IY), установлено их распределение по всем хромосомам генома твердой пшеницы. Основные генетические локусы, определяющие более 60 % варьирования признака, были картированы в хромосомах 7AL и 7BL. Вклад этих локусов связан с аллельными вариациями, влияющими на активность фермента фитоенсинтетазы (PSY). В других хромосомах были локализованы минорные генетические факторы, из которых наиболее значимы QTL, расположенные в хромосомах 3AS (ассоциирован с геном LCYE-ликопин- ε-циклаза) и 4ВS (аллель Lpx-B1.1c). При этом показано, что аллель Lpx-B1.1c вносит вклад в снижение актив- ности липоксигеназы, окисляющей каротиноиды в процессе изготовления конечных продуктов. Рассмотрены и обсуждены проблемы использования молекулярных маркеров в селекционных программах, нацеленных на увеличение концентрации пигментов в зерне и улучшение цветовых характеристик пасты.

Cortical distribution of GABAergic interneurons is determined by migration time and brain size

Cortical interneurons (CINs) originate in the ganglionic eminences (GEs) and migrate tangentially to the cortex guided by different attractive and repulsive cues. Once inside the cortex, the cellular and molecular mechanisms determining the migration of CINs along the rostrocaudal axis are less well understood. Here, we investigated the cortical distribution of CINs originating in the medial and caudal GEs at different time points. Using molecular and genetic labeling, we showed that, in the mouse, early- and late-born CINs (E12 versus E15) are differentially distributed along the rostrocaudal axis. Specifically, late-born CINs are preferentially enriched in cortical areas closer to their respective sites of origin in the medial or caudal GE. Surprisingly, our in vitro experiments failed to show a preferential migration pattern along the rostrocaudal axis for medial- or caudal-born CINs. Moreover, in utero transplantation experiments suggested that the rostrocaudal dispersion of CINs depends on the developmental stage of the host brain and is limited by the migration time and the increasing size of the developing brain. These data suggest that the embryonic expansion of the cortex contributes to the rostrocaudal distribution of CINs.

Elasticizing tissues for reversible shape transformation and accelerated molecular labeling.

We developed entangled link-augmented stretchable tissue-hydrogel (ELAST), a technology that transforms tissues into elastic hydrogels to enhance macromolecular accessibility and mechanical stability simultaneously. ELASTicized tissues are highly stretchable and compressible, which enables reversible shape transformation and faster delivery of probes into intact tissue specimens via mechanical thinning. This universal platform may facilitate rapid and scalable molecular phenotyping of large-scale biological systems, such as human organs.

Enhanced Red Fluorescence Emissions of [Ru(bpy)<sub>3</sub>]Cl<sub>2</sub> in DNA Complexes

The research on molecular devices, fluorescent labels and fluorescent probes based on the interaction between biomolecular DNA and fluorescent dyes has been paid more attention at home and abroad. In this paper, the luminescence properties of the [Ru(bpy)3]Cl2 complex itself were investigated, and the luminescence properties of the [Ru(bpy)3]Cl2 complex under the interaction of the solution and the film were observed by association of the DNA complex with the [Ru(bpy)3]Cl2 complex. The results showed that [Ru(bpy)3]Cl2 emitted red light with its main emission peak wavelength was 610nm, and its fluorescence intensity was the highest when the concentration of solution substance was 10mmol/L. When doped with DNA solution in [Ru(bpy)3]Cl2 complex, a small amount of fluorescent dye [Ru(bpy)3]Cl2 can be used to achieve a higher luminous intensity At the same time, the fluorescent dye [Ru(bpy)3]Cl2 doped with DNA solution reached a higher luminous intensity in the thin-film state. This experiment provides an important experimental basis for the application of fluorescent substance [Ru(bpy)3]Cl2 in luminescent thin films.

Advances in Optical Single-Molecule Detection: En Route to Supersensitive Bioaffinity Assays.

The ability to detect low concentrations of analytes and in particular low‐abundance biomarkers is of fundamental importance, e.g., for early‐stage disease diagnosis. The prospect of reaching the ultimate limit of detection has driven the development of single‐molecule bioaffinity assays. While many review articles have highlighted the potentials of single‐molecule technologies for analytical and diagnostic applications, these technologies are not as widespread in real‐world applications as one should expect. This Review provides a theoretical background on single‐molecule—or better digital—assays to critically assess their potential compared to traditional analog assays. Selected examples from the literature include bioaffinity assays for the detection of biomolecules such as proteins, nucleic acids, and viruses. The structure of the Review highlights the versatility of optical single‐molecule labeling techniques, including enzymatic amplification, molecular labels, and innovative nanomaterials.

Zwitterion and Oligo(ethylene glycol) Synergy Minimizes Nonspecific Binding of Compact Quantum Dots.

Quantum dots (QDs) are a class of fluorescent nanocrystals in development as labels for molecular imaging in cells and tissues. Recently, coatings for quantum dots based on multidentate polymers have improved labeling performance in a range of bioanalytical applications, primarily due to reduced probe hydrodynamic size. Now, an ongoing challenge is to eliminate nonspecific binding between these small probes and cellular components that mask specifically labeled molecules. Here, we describe insights into controlling and minimizing intermolecular interactions governing nonspecific binding using multidentate polymers with tunable hydrophilic functional groups that are cationic, anionic, zwitterionic (ZW), or nonionic (oligoethylene glycol; OEG). By fixing surface-binding groups and polymer length, coated colloids have similar sizes but diverse physicochemical properties. We measure binding to globular proteins, fixed cells, and living cells and observe a substantial improvement in nonspecific binding resistance when surfaces are functionalized with a combination of ZW and OEG. The independent underlying effects of counterion adsorption and flexibility appear to synergistically resist adsorption when combined, particularly for fixed cells enriched in both charged and hydrophobic moieties. We further show that ZW-OEG QDs are stable under diverse conditions and can be self-assembled with antibodies to specifically label surface antigens on living cells and cytoplasmic proteins in fixed cells. This surface engineering strategy can be adopted across the diverse range of colloidal materials currently in use and in development for biomedical applications to optimize their molecular labeling specificity.

2-Butyl-2-tert-butyl-5,5-diethylpyrrolidine-1-oxyls: Synthesis and Properties.

Nitroxides are broadly used as molecular probes and labels in biophysics, structural biology, and biomedical research. Resistance of a nitroxide group bearing an unpaired electron to chemical reduction with low-molecular-weight antioxidants and enzymatic systems is of critical importance for these applications. The redox properties of nitroxides are known to depend on the ring size (for cyclic nitroxides) and electronic and steric effects of the substituents. Here, two highly strained nitroxides, 5-(tert-butyl)-5-butyl-2,2-diethyl-3-hydroxypyrrolidin-1-oxyl (4) and 2-(tert-butyl)-2-butyl-5,5-diethyl-3,4-bis(hydroxymethyl)pyrrolidin-1-oxyl (5), were prepared via a reaction of the corresponding 2-tert-butyl-1-pyrroline 1-oxides with butyllithium. Thermal stability and kinetics of reduction of the new nitroxides by ascorbic acid were studied. Nitroxide 5 showed the highest resistance to reduction.

Detecting Protein-Ligand Interaction from Integrated Transient Induced Molecular Electronic Signal (i-TIMES).

Quantitative information about protein-ligand interactions is central to drug discovery. To obtain the quintessential reaction dissociation constant, ideally measurements of reactions should be performed without perturbations by molecular labeling or immobilization. The technique of transient induced molecular electrical signal (TIMES) has provided a promising technique to meet such requirements, and its performance in a microfluidic environment further offers the potential for high throughput and reduced consumption of reagents. In this work, we further the development by using integrated TIMES signal (i-TIMES) to greatly enhance the accuracy and reproducibility of the measurement. While the transient response may be of interest, the integrated signal directly measures the total amount of surface charge density resulted from molecules near the surface of electrode. The signals enable quantitative characterization of protein-ligand interactions. We have demonstrated the feasibility of i-TIMES technique using different biomolecules including lysozyme, N,N',N″-triacetylchitotriose (TriNAG), aptamer, p-aminobenzamidine (pABA), bovine pancreatic ribonuclease A (RNaseA), and uridine-3'-phosphate (3'UMP). The results show i-TIMES is a simple and accurate technique that can bring tremendous value to drug discovery and research of intermolecular interactions.

Single-Molecule Imaging and Labelling with DNA-Based Superresolution Microscopy

Recent advances in localisation-based super-resolution microscopy have enabled researchers to visualise single molecular features down to individual molecular components (∼5 nm), but do not yet allow manipulation of single-molecule targets in a user-prescribed, context-dependent manner. Here we report an “Action-PAINT” strategy for super-resolution labelling upon visualisation on single molecules. This approach monitors and localises DNA binding events in real-time with DNA-PAINT, and upon visualisation of binding to a desired location, photo-crosslinks the DNA to affix the molecular label. We showed the efficiency of 3-cyanovinylcarbazole nucleoside (CNVK) photo-inducible crosslinking on single molecular targets and developed a software package for real-time super-resolution imaging and crosslinking control. We then benchmarked our super-resolution labelling method on synthetic DNA nanostructures and demonstrated targeted multi-point labelling on various complex patterns with 30 nm selectivity. Finally, we performed targeted in situ labelling on fixed microtubule samples with 40 nm target size and custom-controlled, sub-diffraction spacing.

Short-Wave Infrared Quantum Dots with Compact Sizes as Molecular Probes for Fluorescence Microscopy.

Materials with short-wave infrared (SWIR) emission are promising contrast agents for in vivo animal imaging, providing high-contrast and high-resolution images of blood vessels in deep tissues. However, SWIR emitters have not been developed as molecular labels for microscopy applications in the life sciences, which require optimized probes that are bright, stable, and small. Here, we design and synthesize semiconductor quantum dots (QDs) with SWIR emission based on HgxCd1-xSe alloy cores red shifted to the SWIR by epitaxial deposition of thin HgxCd1-xS shells with a small band gap. By tuning alloy composition alone, the emission can be shifted across the visible-to-SWIR (VIR) spectra while maintaining a small and equal size, allowing direct comparisons of molecular labeling performance across a broad range of wavelength. After coating with click-functional multidentate polymers, the VIR-QD spectral series has high quantum yield in the SWIR (14-33%), compact size (13 nm hydrodynamic diameter), and long-term stability in aqueous media during continuous excitation. We show that these properties enable diverse applications of SWIR molecular probes for fluorescence microscopy using conjugates of antibodies, growth factors, and nucleic acids. A broadly useful outcome is a 10-55-fold enhancement of the signal-to-background ratio at both the single-molecule level and the ensemble level in the SWIR relative to visible wavelengths, primarily due to drastically reduced autofluorescence. We anticipate that VIR-QDs with SWIR emission will enable ultrasensitive molecular imaging of low-copy number analytes in biospecimens with high autofluorescence.

Costless Performance Improvement in Machine Learning for Graph-Based Molecular Analysis

Graph neural networks (GNNs) have attracted significant attention from the chemical science community because molecules can be represented as a featured graph. In particular, graph convolutional network (GCN) and its variants have been widely used and have shown a state-of-the-art performance in analyzing molecules, such as molecular label classification, drug discovery, and molecular property prediction. However, in molecular analysis, existing GCNs have two fundamental limitations: (1) information of the molecular scale is distorted and (2) global structures in a molecule are ignored. These limitations can seriously degrade the performance in the machine learning-based molecular analysis because the scale and global structure information of a molecule occasionally have a significant effect on the molecular properties. To overcome the limitations of existing GCNs, we comprehensively analyzed the structure of GCNs and developed a costless solution for the limitations of GCNs. To demonstrate the effectiveness of our solution, extensive experiments were conducted on various benchmark datasets.

Disruption of hepatic small heterodimer partner induces dissociation of steatosis and inflammation in experimental nonalcoholic steatohepatitis

Disruption of hepatic small heterodimer partner induces dissociation of steatosis and inflammation in experimental nonalcoholic steatohepatitis

Molecular Labeling of DNA Amyloid Sensor with Plasma, and the Glycemic Factor, for Photonic Detection of Alzheimer's in Blood

Molecular Labeling of DNA Amyloid Sensor with Plasma, and the Glycemic Factor, for Photonic Detection of Alzheimer's in Blood

Signal to Noise Ratio as a Cross-Platform Metric for Intraoperative Fluorescence Imaging.

Real-time molecular imaging to guide curative cancer surgeries is critical to ensure removal of all tumor cells; however, visualization of microscopic tumor foci remains challenging. Wide variation in both imager instrumentation and molecular labeling agents demands a common metric conveying the ability of a system to identify tumor cells. Microscopic disease, comprised of a small number of tumor cells, has a signal on par with the background, making the use of signal (or tumor) to background ratio inapplicable in this critical regime. Therefore, a metric that incorporates the ability to subtract out background, evaluating the signal itself relative to the sources of uncertainty, or noise is required. Here we introduce the signal to noise ratio (SNR) to characterize the ultimate sensitivity of an imaging system and optimize factors such as pixel size. Variation in the background (noise) is due to electronic sources, optical sources, and spatial sources (heterogeneity in tumor marker expression, fluorophore binding, and diffusion). Here, we investigate the impact of these noise sources and ways to limit its effect on SNR. We use empirical tumor and noise measurements to procedurally generate tumor images and run a Monte Carlo simulation of microscopic disease imaging to optimize parameters such as pixel size.

Pre-aggregation of scalp progenitor dermal and epidermal stem cells activates the WNT pathway and promotes hair follicle formation in in vitro and in vivo systems

BackgroundBillions of dollars are invested annually by pharmaceutical companies in search of new options for treating hair loss conditions; nevertheless, the challenge remains. One major limitation to hair follicle research is the lack of effective and efficient drug screening systems using human cells. Organoids, three-dimensional in vitro structures derived from stem cells, provide new opportunities for studying organ development, tissue regeneration, and disease pathogenesis. The present study focuses on the formation of human hair follicle organoids.MethodsScalp-derived dermal progenitor cells mixed with foreskin-derived epidermal stem cells at a 2:1 ratio aggregated in suspension to form hair follicle-like organoids, which were confirmed by immunostaining of hair follicle markers and by molecular dye labeling assays to analyze dermal and epidermal cell organization in those organoids. The hair-forming potential of organoids was examined using an in vivo transplantation assay.ResultsPre-aggregation of dermal and epidermal cells enhanced hair follicle formation in vivo. In vitro pre-aggregation initiated the interactions of epidermal and dermal progenitor cells resulting in activation of the WNT pathway and the formation of pear-shape structures, named type I aggregates. Cell-tracing analysis showed that the dermal and epidermal cells self-assembled into distinct epidermal and dermal compartments. Histologically, the type I aggregates expressed early hair follicle markers, suggesting the hair peg-like phase of hair follicle morphogenesis. The addition of recombinant WNT3a protein to the medium enhanced the formation of these aggregates, and the Wnt effect could be blocked by the WNT inhibitor, IWP2.ConclusionsIn summary, our system supports the rapid formation of a large number of hair follicle organoids (type I aggregates). This system provides a platform for studying epithelial-mesenchymal interactions, for assessing inductive hair stem cells and for screening compounds that support hair follicle regeneration.

Endothelial IL-8 induced by porcine circovirus type 2 affects dendritic cell maturation and antigen-presenting function

BackgroundPorcine circovirus (PCV) disease caused by PCV type 2 (PCV2) is mainly attributed to immunosuppression and immune damage. PCV2 can infect vascular endothelial cells and induce high expression of endothelial IL-8. Dendritic cells (DCs), as professional antigen-presenting cells, can not only present antigens but also activate naïve T-cells, causing an immune response.MethodsTo demonstrate whether endothelial IL-8 is the main factor inhibiting the maturation and related functions of dendritic cells during PCV2 infection, monocyte-derived DCs (MoDCs) and porcine iliac artery endothelial cells (PIECs) processed by different methods were co-cultured in two ways. Flow cytometry, molecular probe labeling, fluorescence quantitative PCR, and the MTS assay were used to detect the changes in related functions and molecules of MoDCs.ResultsCompared to those in the PIEC-DC group, the endothelial IL-8 upregulation co-culture group showed significantly lower double-positive rates for CD80/86 and MHC-II of MoDCs and significantly increased endocytosis of MoDCs. Meanwhile, the adhesion rate and average fluorescence intensity of MoDCs were significantly downregulated in migration and adhesion experiments. Furthermore, the MHC-I and LAMP7 mRNA levels in MoDCs and the proliferation of MoDC-stimulated T-cells were markedly reduced. However, the changes in MoDCs of the endothelial IL-8 downregulation co-culture group were the opposite.ConclusionsPCV2-induced endothelial IL-8 reduces the adhesion and migration ability of MoDCs, resulting in a decreased maturation rate of MoDCs, and further inhibits antigen presentation by DCs. These results may explain the immunosuppressive mechanism of PCV2 from the perspective of the interaction between endothelial cells and DCs in vitro.