Ordered Porous Layer Interferometry for Dynamic Observation of Non-Specific Adsorption Induced by 1-Ethyl-3-(3-(dimethylamino)propyl) Carbodiimide.

Nonspecific adsorption (NSA) seems to be an impregnable obstacle to the progress of the biomedical, diagnostic, microelectronic, and material fields. The reaction path of bioconjugation can alter the surface charge distribution on products and the interaction of bioconjugates, an ignored factor causing NSA. We monitored exacerbated NSA introduced by a 1-ethyl-3-(3-(dimethylamino)propyl) carbodiimide (EDC) addition reaction, which cannot be resistant to bovine serum albumin (BSA) or polyethylene glycol (PEG) antifouling coating and Tween-20. And the negative effects can be minimized by adding as low as 7.5 × 10-6 M N-hydroxysulfosuccinimide (sulfo-NHS). We applied ordered porous layer interferometry (OPLI) to sensitively evaluate the NSA that is difficult to measure on individual particles. Using the silica colloidal crystal (SCC) film with Fabry-Perot fringes as in situ and real-time monitoring for the NSA, we optimized the surface chemistry to yield a conjugate surface without variational charge distribution. In this work, we propose a novel approach from the perspective of the reaction pathway to minimize the NSA of solely EDC-induced chemistry.

From Self-Assembly of Colloidal Crystals toward Ordered Porous Layer Interferometry.

Interferometry-based, reflectometric, label-free biosensors have made significant progress in the analysis of molecular interactions after years of development. The design of interference substrates is a key research topic for these biosensors, and many studies have focused on porous films prepared by top-down methods such as porous silicon and anodic aluminum oxide. Lately, more research has been conducted on ordered porous layer interferometry (OPLI), which uses ordered porous colloidal crystal films as interference substrates. These films are made using self-assembly techniques, which is the bottom-up approach. They also offer several advantages for biosensing applications, such as budget cost, adjustable porosity, and high structural consistency. This review will briefly explain the fundamental components of self-assembled materials and thoroughly discuss various self-assembly techniques in depth. We will also summarize the latest studies that used the OPLI technique for label-free biosensing applications and divide them into several aspects for further discussion. Then, we will comprehensively evaluate the strengths and weaknesses of self-assembly techniques and discuss possible future research directions. Finally, we will outlook the upcoming challenges and opportunities for label-free biosensing using the OPLI technique.

Real-time monitoring of papain digestion of antibodies immobilized with various strategies by optical interferometry.

Antigen binding fragments (Fabs) employed in research are typically generated by the papain digestion of monoclonal antibodies. However, the interaction between papain and antibodies at the interface remains unclear. Herein, we developed ordered porous layer interferometry for the label-free monitoring of the interaction between the antibody and papain at liquid-solid interfaces. Human immunoglobulin G (hIgG) was used as the model antibody, and different strategies were employed to immobilize it on the surface of silica colloidal crystal (SCC) films which are optical interferometric substrates. It was observed that different immobilization strategies induced different changes in the optical thickness (OT) of SCCs. The order of rate of the changes of OT from largest to smallest was IgG immobilized by protein A orientation, glutaraldehyde coupling, and physical adsorption. This phenomenon can be explained by the varied orientations of the antibodies created at the interface by the different modification procedures. The Fab-up orientation maximized the exposure of the hinge region sulfhydryl group and easily underwent conformational transitions because hIgG was immobilized by protein A. This process stimulates papain to produce the highest degree of activity, resulting in the greatest decrease in OT. This study provides insights into the catalysis of papain on antibodies.

Evaluation of covalent coupling strategies for immobilizing ligands on silica colloidal crystal films by optical interferometry.

Immobilizing ligands is a crucial part of preparing optical sensors and directly connected to the sensitivity, stability, and other characteristics of sensors. In this work, an ordered porous layer interferometry (OPLI) system that can monitor the covalent coupling process of ligands in real time was developed. Films of silica colloidal crystal (SCC), as optical interference substrates, were surface modified by three different reagents: chloroacetic acid, glutaric anhydride, and carboxymethyl dextran. Staphylococcus aureus protein A (SPA), the ligand, was immobilized on SCC films. The covalent coupling process of SPA and SCC films can be dynamically monitored by the OPLI system. In addition, the three different strategies were evaluated by comparing the efficiency of the sensors prepared by different methods for binding Immunoglobulin G (IgG). The glutaric anhydride-modified sensor offers apparent advantages in terms of bound IgG quantity and affinity. This system provides a simple and intuitive way to determine the efficiency of different covalent coupling strategies. Furthermore, the sensor covalently coupled with SPA also excels in the determination of IgG content in complex systems such as milk. At the same time, the covalent coupling gives the sensor the ability to be stored stably over time.

Monitoring of silica colloidal crystal-embedded chitosan hydrogel films swelling and its drug release application.

The hydrogels, because of their swelling properties in response to the environmental stimulus, are being widely considered for the design of controlled drug release systems. To meet the need for developing effective drug delivery methods, we developed special silica colloidal crystal (SCC)-embedded chitosan hydrogel films. The SCC films served as an interference substrate and drug storage layer, while the chitosan hydrogel served as a cover to regulate the drug release. The optical interferometry was performed to dynamically monitor the volume phase transition of chitosan hydrogel response to pH stimulation. Furthermore, the effects of crosslinking ratio and hydrogel thickness on the swelling properties of chitosan hydrogel were also evaluated. More importantly, the pH-responsive swelling of chitosan hydrogel was used to slowly release indomethacin. This system may provide support for drug delivery studies, therefore further expected to apply in the enhancement of the treatment efficiency of new drug therapies.

Real-Time Monitoring of Curcumin Release with a Lipid-Curcumin-Loaded Silica Colloidal Crystal Film Using Optical Interferometry.

A novel efficacious strategy for real-time monitoring of the release of hydrophobic cargo curcumin (molecule model nutraceuticals) from a lipid-curcumin-loaded silica colloidal crystal (L(Cur)-SCC) film controlled by lipase was developed. Curcumin was dispersed in a proportion of a digestible lipid complex (glycerol trioleate and glycerol tristearate) to prepare a lipid-curcumin complex and then loaded into the SCC film by a capillary to prepare an L(Cur)-SCC film. Lipase-triggered degradation of the digestible lipid complex resulted in curcumin release being tracked in real-time by ordered porous layer interferometry (OPLI). The optical thickness changes (ΔOT) of the L(Cur)-SCC film depend on the mass changes of the lipid-curcumin complex due to the migration of interference fringes caused by the lipase degradation of the digestible lipid complex. Curcumin release from the L(Cur)-SCC film was characterized and analyzed in combination with an ultraviolet-visible spectrophotometer, a nanoparticle size analyzer, and an attenuated total reflection infrared spectrometer. The introduction of a soluble dietary fiber (pectin) into the L(Cur)-SCC film delayed the release rate of curcumin. Furthermore, the real-time sustained release of curcumin from the L(Cur)-SCC film in the simulated digestive fluids was tracked. This study provides an early exploration of the real-time controlled release of lipid-soluble nutraceuticals in the gastrointestinal tract.

Real-time kinetics and affinity analysis of the interaction between protein A and immunoglobulins G derived from different species on silica colloidal crystal films.

Kinetic and affinity analysis of protein interactions reveals information on their related activities in biological processes. Herein, we established a system for evaluating the kinetics and affinity of the interaction between protein A and various IgG species on the surface of silica spheres of silica colloidal crystal (SCC) films by the extraordinary optical interference capabilities of 190 nm silica spheres after self-assembly. The equilibrium association constant (KA) was calculated by the equilibrium Langmuir model and nonlinear least-squares analysis of time-dependent data. The relative protein A/IgG binding affinity is human > rabbit >cow >goat. In addition, the competitive interaction of distinct species of IgG with protein A at the interface of SCC films was studied and performed. These findings may help with the use of protein A and other recognition components in a number of sensor types. Furthermore, this research might offer a novel approach to determining the kinetics and affinity of proteins on the surface of spheres particles, which may contribute to the development of the application of spheres particles in pharmaceutical science, biomedical engineering, and other techniques.

Insights into the interaction between chitosan and pepsin by optical interferometry.

Polysaccharides and proteins have attracted increasing interest in the fields of biomedicine and green chemical as biocomposites due to their inherent versatility. Here, we used silica colloidal crystal (SCC) films combined with an ordered porous layer interferometry (OPLI) method to investigate the interaction between chitosan and pepsin at different concentrations and pH values in real time. Zeta potential was combined with attenuated total reflection Fourier transform infrared spectroscopy (ATR-FTIR) and Fourier transform infrared microscopy (FTIR microscopy) to illustrate the interaction mechanism further. The results showed that the variation and slope of the optical thickness (OT) caused by the Fabry-Perot fringes represent the degree and process of interaction. The protonation of chitosan and the net charge carried by pepsin caused various degrees of electrostatic attraction under different pH values. Meanwhile, the rate and degree of hydrolysis were positively correlated with pepsin concentration. This work results provide a theoretical basis for designing novel composites based on the development of polysaccharides and proteins.

Construction of lipid layer and monitoring its digestion by optical interferometry.

A method for real-time monitoring of lipid digestion based on photonic crystals formed from silica was developed. As an effective "net", the highly ordered silica colloidal crystal (SCC) film provides structural support for lipid payload. This method based on optical interferometric film kinetics was used to record the whole kinetics progress of olive oil hydrolysis by lipase in real time and calculate the kinetic Michaelis constant. The kinetic parameters were compared with the results determined by the titration method. The effects of bile salt content on lipase and olive oil layer were studied. This method provides a potential evaluation system for real-time digestion and degradation of edible oil in the food field. It also provides a basis for further real-time evaluation of lipid bioavailability in food systems by real-time recording the release and degradation of lipids in the food nano-matrix.

Real-time monitoring of immunoglobulin G levels in milk using an ordered porous layer interferometric optical sensor.

Immunoglobulin G (IgG) is a significant ingredient of immunological activity in milk and colostrum, the activity and content of which is easily disturbed by potentially conditional variant during sterilization. Therefore, developing robust methods for the detection of IgG levels in milk is especially important. Herein, protein A from the Staphylococcus aureus functionalized silica colloidal crystalline film (SCC@SPA) sensing unit combined with ordered porous layer interferometry (OPLI) for IgG detection in untreated bovine milk was developed. Calibration curves in milk and buffer were set up by the variations of the optical thickness (OT) of the sensing unit after the IgG association and dissociation phases. The influence of temperature on the level of IgG was evaluated. Furthermore, the identification of IgG levels with pasteurized milk and ultrahigh temperature (UHT) sterilized milk from the market randomly was successfully carried out without any sample pretreatment. More importantly, compared with other methods, this novel method has the advantages of convenient operation, low cost, and suitability for point-of-care (POC) testing.

Construction of Optical Interference Fibrin and Thrombolysis Analysis with Silica Colloidal Crystal Films.

Developing powerful real-time methods for monitoring the thrombolytic process is highly desirable for the early therapy of thrombus diseases. Herein, an optical interference fibrin was constructed, fabricated by assembling a 190 nm silica colloidal crystal on glass slides, for detecting a thrombolytic process through the shift of interference peaks caused by the variation of the thicknesses of a silica colloidal crystal film with loaded fibrin dissolution. The whole kinetic progress of thrombolysis by nattokinase and urokinase as thrombolytic drug models was recorded, and the kinetic data were calculated. Moreover, the developed method shows excellent sensitivity for the activity of nattokinase and urokinase with wide linear ranges of approximately 0.75-750 and 5-1000 units mL-1, respectively. Thus, this method can be used as a real-time, low-cost, and simple system for monitoring the thrombolytic process of drugs, demonstrating huge potential in the development of treating thromboembolic diseases and screening drugs.

Effect of Relative Humidity on the Thickness of Assembled Silica Colloidal Crystal Films.

In order for the colloidal crystal films to be better applied, the influence of relative humidity on the preparation of silica colloidal crystal (SCC) films was systematically studied to solve the problem of different thicknesses of SCC films prepared by different batches under the conditions with the same temperature, concentration of suspension and diameter of the particles. SCC films with 190 nm particles were prepared by static vertical deposition method under different humidity regulated by saturated salt solutions, and the thickness of the films was obtained by an interferometric method. The results showed that the increase in humidity would reduce the thickness of the prepared films, which was believed to be caused by the decrease in evaporation rate after the wetting film absorbs water vapor. A new formula for calculating film thickness was proposed and verified from a series of experiments. With the control of humidity, high-quality SCC films with controlled thickness can be repeatedly prepared.

Using Reflectometric Interference Spectroscopy to Real-Time Monitor Amphiphile-Induced Orientational Responses of Liquid-Crystal-Loaded Silica Colloidal Crystal Films.

An approach to optical transduction and amplification of amphiphile-triggered orientational responses of liquid crystals (LCs) based on the interference effect was developed. The sensitive substrate was obtained by lading 4'-pentyl-4-cyanobiphenyl (5CB) into three-dimensionally ordered silica colloidal crystal (SCC) films. Changes in the optical thickness (ΔOT) of the substrates, which are inverted by their Fabry-Perot fringes, depend on the changes of the refractive index caused by the differences in the orientations of LCs. The orientation changes of LCs loading into SCC films have the effect of amplifying signals. These are based on the interactions between surfactants (alkyl trimethylammonium halides (CnTABs, n = 8, 10, 12, 14, and 16) and sodium lauryl sulfonate (SLS)) and LCs, which induce a particular orientation of the LCs molecules. In this flowing system, the reversibility of the signal response for the adsorption of amphiphile was related to the length of the surfactant chain and its critical micelle concentration (CMC). A new method capable of real-time sensing adsorbate-triggered anchoring transitions based on LC-infiltrated SCC films was accomplished. These results provide basics and principles for online, label-free, and real-time analysis of molecules and their interactions in a flowing environment based on the interference effect.

Real-Time and Label-Free Monitoring of Biomolecular Interactions within Complex Biological Media Using a Silica Colloidal Crystal Film.

A method capable of real-time and label-free monitoring of biomolecular interactions within whole blood, without any sample separation and label process, is described. This was accomplished using silica colloidal crystal (SCC) films, three-dimensionally ordered silica particle arrays whose interference effect is a function of their optical thickness, as interference-sensitive substrates. Interactions between immunoglobulin G (IgG) and protein A from Staphylococcus aureus (SPA) conjugates with changes in the optical thickness of SCC films were monitored spectroscopically. Successful detection of IgG was achieved in the buffer and whole blood. This system constitutes a simple label-free analysis showing great potential in monitoring interactions between biomolecules in complex biological media.

Immunoregenerative effects of the bionically cultured Sanghuang mushrooms (Inonotus sanghuagn) on the immunodeficient mice.

ETHNOPHARMACOLOGICAL RELEVANCE: Description of the pharmacological activities of Sanghuang mushrooms (Inonotus Sanghuang) can be traced back to Tang dynasty of China 1300 years ago. This mushroom has been widely accepted in China, Japan, Korea and certain regions of Europe as a nutraceutical medicine for enhancing immunity or an alternative medicine for prevention or inhibition of tumorigenesis. However, this mushroom is rarely available from the mulberry trees in the wild because of the rigorous conditions needed for formation of the Sanghuang mushrooms. AIM OF THE STUDY: This study aims to establish a practical protocol for culture, particularly for a bunch of production of Sanghuang mushrooms possibly to commercialize the cultured Sanghuang based on deep comparison of quality and pharmacological activities between the cultured and the wild Sanghuang. MATERIALS AND METHODS: A phylogenetic tree containing five strains of the wild Sanghuang was constructed using rDNA markers. Different temperatures and medium compositions were surveyed to develop a practical protocol for culture of the Sanghuang mushrooms. 5-fluorouracil was used to induce the immunodeficient mice. Chemotherapeutic components and pharmacological activities were deeply analyzed between a cultured strain (SG) and three strains of the wild Sanghuang. RESULTS: Maintenance of a temperature of 22-28 °C and a high relative humidity of 90-95%, and use of a high ratio (80%) of mulberry tree sticks in the medium were critical to successful culture of Sanghuang. The cultured mushrooms were yellow with a uniform shape, while the wild Sanghuang was dark brown with a smaller and irregular shape. The cultured mushrooms contained significantly higher levels of polysaccharides, amino acids, and water-soluble nutraceuticals, whereas flavones in the wild Sanghuang were significantly higher (P < 0.05). Use of a dose of 8 mg/kg or 16 mg/kg to immunoregenerate the immunodeficient mice was comparable between the cultured and wild Sanghang based on analysis of hematological parameters and histological examination of the thymus and spleen in the treated mice. CONCLUSIONS: This study highlights the potential of the immunoregenerative functions of the cultured Sanghuang for cancer chemotherapy and suggests that the cultured Sanghuang can be an alternative to wild Sanghuang used for nutraceutical medicine.

Interference Effect of Silica Colloidal Crystal Films and Their Applications to Biosensing.

With the aim to develop better and more reliable interference effective substrates, silica colloidal crystal films with different sphere diameters and film thicknesses were successfully made by an improved vertical deposition method and a systematic investigation of their reflectometric interference spectroscopy (RIfS) properties are presented in this work. The influence of silica sphere diameter and film thickness on the RIfS signals was studied. The results showed that the film thickness is the key factor of RIfS signals. An RIfS system was set up by using a silica colloidal crystal film as an interference effective substrate. The influence of film thickness on the response to refractive index changes of the proposed system was also investigated. When the influence of film thickness on RIfS signals and refractive index response we considered together, silica colloidal crystal films with a thickness between 4 and 6 µm were chosen for sensor construction. Monitoring the digestive process of gelatin with trypsin was also demonstrated by combining gelatin-modified silica colloidal crystal films with RIfS. The system showed excellent sensitivity with a wide linear range and could achieve real-time measurement of each process. It has been proved that this is a promising method to construct biosensors using silica colloidal crystal films as interference-sensitive substrates.

Arabidopsis Duodecuple Mutant of PYL ABA Receptors Reveals PYL Repression of ABA-Independent SnRK2 Activity.

Abscisic acid (ABA) is an important phytohormone controlling responses to abiotic stresses and is sensed by proteins from the PYR/PYL/RCAR family. To explore the genetic contribution of PYLs toward ABA-dependent and ABA-independent processes, we generated and characterized high-order Arabidopsis mutants with mutations in the PYL family. We obtained a pyl quattuordecuple mutant and found that it was severely impaired in growth and failed to produce seeds. Thus, we carried out a detailed characterization of a pyl duodecuple mutant, pyr1pyl1/2/3/4/5/7/8/9/10/11/12. The duodecuple mutant was extremely insensitive to ABA effects on seed germination, seedling growth, stomatal closure, leaf senescence, and gene expression. The activation of SnRK2 protein kinases by ABA was blocked in the duodecuple mutant, but, unexpectedly, osmotic stress activation of SnRK2s was enhanced. Our results demonstrate an important role of basal ABA signaling in growth, senescence, and abscission and reveal that PYLs antagonize ABA-independent activation of SnRK2s by osmotic stress.

High-throughput m6A-seq reveals RNA m6A methylation patterns in the chloroplast and mitochondria transcriptomes of Arabidopsis thaliana.

This study is the first to comprehensively characterize m6A patterns in the Arabidopsis chloroplast and mitochondria transcriptomes based on our open accessible data deposited in NCBI's Gene Expression Omnibus with GEO Series accession number of GSE72706. Over 86% of the transcripts were methylated by m6A in the two organelles. Over 550 and 350 m6A sites were mapped, with ~5.6 to ~5.8 and ~4.6 to ~4.9 m6A sites per transcript, to the chloroplast and mitochondria genome, respectively. The overall m6A methylation extent in the two organelles was greatly higher than that in the nucleus. The m6A motif sequences in the transcriptome of two organelles were similar to the nuclear motifs, suggesting that selection of the m6A motifs for RNA methylation was conserved between the nucleus and organelle transcriptomes. The m6A patterns of rRNAs and tRNAs in the organelle were similar to those in the nucleus. However, the m6A patterns in coding RNAs were distinct between the nucleus and the organelle, suggesting that that regulation of the m6A methylation patterns may be different between the nuclei and the organelles. The extensively methylated transcripts in the two organelles were mainly associated with rRNA, ribosomal proteins, photosystem reaction proteins, tRNA, NADH dehydrogenase and redox. On average, 64% and 79% of the transcripts in the two organelles showed differential m6A methylation across three organs of the leaves, flowers and roots. The m6A methylation extent in the chloroplast was higher than that in the mitochondria. This study provides deep insights into the m6A methylation topology and differentiation in the plant organelle transcriptomes.

High throughput deep degradome sequencing reveals microRNAs and their targets in response to drought stress in mulberry (Morus alba).

MicroRNAs (miRNAs) play important regulatory roles by targeting mRNAs for cleavage or translational repression. Identification of miRNA targets is essential to better understanding the roles of miRNAs. miRNA targets have not been well characterized in mulberry (Morus alba). To anatomize miRNA guided gene regulation under drought stress, transcriptome-wide high throughput degradome sequencing was used in this study to directly detect drought stress responsive miRNA targets in mulberry. A drought library (DL) and a contrast library (CL) were constructed to capture the cleaved mRNAs for sequencing. In CL, 409 target genes of 30 conserved miRNA families and 990 target genes of 199 novel miRNAs were identified. In DL, 373 target genes of 30 conserved miRNA families and 950 target genes of 195 novel miRNAs were identified. Of the conserved miRNA families in DL, mno-miR156, mno-miR172, and mno-miR396 had the highest number of targets with 54, 52 and 41 transcripts, respectively, indicating that these three miRNA families and their target genes might play important functions in response to drought stress in mulberry. Additionally, we found that many of the target genes were transcription factors. By analyzing the miRNA-target molecular network, we found that the DL independent networks consisted of 838 miRNA-mRNA pairs (63.34%). The expression patterns of 11 target genes and 12 correspondent miRNAs were detected using qRT-PCR. Six miRNA targets were further verified by RNA ligase-mediated 5' rapid amplification of cDNA ends (RLM-5' RACE). Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that these target transcripts were implicated in a broad range of biological processes and various metabolic pathways. This is the first study to comprehensively characterize target genes and their associated miRNAs in response to drought stress by degradome sequencing in mulberry. This study provides a framework for understanding the molecular mechanisms of drought resistance in mulberry.

Transcriptome-wide high-throughput deep m(6)A-seq reveals unique differential m(6)A methylation patterns between three organs in Arabidopsis thaliana.

BACKGROUND: m(6)A is a ubiquitous RNA modification in eukaryotes. Transcriptome-wide m(6)A patterns in Arabidopsis have been assayed recently. However, differential m(6)A patterns between organs have not been well characterized. RESULTS: Over two-third of the transcripts in Arabidopsis are modified by m(6)A. In contrast to a recent observation of m(6)A enrichment in 5' mRNA, we find that m(6)A is distributed predominantly near stop codons. Interestingly, 85 % of the modified transcripts show high m(6)A methylation extent compared to their transcript level. The 290 highly methylated transcripts are mainly associated with transporters, stress responses, redox, regulation factors, and some non-coding RNAs. On average, the proportion of transcripts showing differential methylation between two plant organs is higher than that showing differential transcript levels. The transcripts with extensively higher m(6)A methylation in an organ are associated with the unique biological processes of this organ, suggesting that m(6)A may be another important contributor to organ differentiation in Arabidopsis. Highly expressed genes are relatively less methylated and vice versa, and different RNAs have distinct m(6)A patterns, which hint at mRNA fate. Intriguingly, most of the transposable element transcripts maintained a fragmented form with a relatively low transcript level and high m(6)A methylation in the cells. CONCLUSIONS: This is the first study to comprehensively analyze m(6)A patterns in a variety of RNAs, the relationship between transcript level and m(6)A methylation extent, and differential m(6)A patterns across organs in Arabidopsis.