Immune imprinting: The persisting influence of the first antigenic encounter with rapidly evolving viruses.

Immune imprinting is a phenomenon that stems from the fundamentals of immunological memory. Upon recurrent exposures to an evolving pathogen, the immune system must weigh the benefits of rapidly recalling established antibody repertoires with greater affinity to the initial variant or invest additional time and energy in producing de novo responses specific to the emerging variant. In this review, we delve into the mechanistic complexities of immune imprinting and its role in shaping subsequent immune responses, both de novo and recall, against rapidly evolving respiratory viruses such as influenza and coronaviruses. By exploring the duality of immune imprinting, we examine its potential to both enhance or hinder immune protection against disease, while emphasizing the role of host and viral factors. Finally, we explore how different vaccine platforms may affect immune imprinting and comment on vaccine strategies that can favor de novo variant-specific antibody responses.

Novel Discrete and Imprinted Fluoride-Selective Sensors: Bridging the Gap from DMSO to Aqueous Samples.

Fluoride in drinking water has beneficial or harmful health effects depending on its concentration. This highlights the need for new low-cost and portable sensors capable of in situ monitoring of F- ions. Unfortunately, achieving high levels of water compatibility and fluoride specificity remains a challenge. Here, four new urea-based discrete sensors are prepared and characterized. The sensors containing anthracenyl- (5) and 9H-fluorenyl- (7) signaling units exhibit intense luminescent emissions in dimethyl sulfoxide, the former being particularly sensitive and selective to fluoride. In water, 5 displays a superior sensitivity (871 M-1) and a detection limit (8 µm) below international guidelines, albeit with cross-sensitivity to H2PO4‾. To enhance the performance, 5 and 7 are embedded into a fluoride-imprinted polymeric matrix to give solid-state sensors (5P and 7P, respectively). 5P shows good sensitivity (360 M-1) and specificity in water. Besides, it has a low detection limit (35 µm) and a response linear range (118-6300 µm) encompassing the limit established by the Environmental Protection Agency (211 µm). Furthermore, 5P also displays good reusability and adequate recovery values in real-sample testing (102 ± 2%), constituting the first example of a low-cost anion-imprinted polymeric probe tailored for the selective sensing of fluoride in aqueous samples.

Proliferative arrest induces neuron differentiation and innate immune responses in control and Creutzfeldt-Jakob Disease agent infected rat septal neurons.

Rat post-mitotic septal (SEP) neurons, engineered to conditionally proliferate at 33°C, differentiate when arrested at 37.5°C and can be maintained for weeks without cytotoxic effects. Nine independent cDNA libraries were made to follow arrest-induced neural differentiation and innate immune responses in normal (Nl) uninfected and CJ agent infected SEP cells. Proliferating Nl versus latently infected (CJ-) cells showed few RNA-seq differences. However arrest induced major changes. Normal cells displayed a plethora of anti-proliferative transcripts. Additionally, known neuron differentiation transcripts, e.g., Agtr2, Neuregulin-1, GDF6, SFRP4 and Prnp were upregulated. These Nl neurons also displayed many activated IFN innate immune genes, e.g., OAS1, RTP4, ISG20, GTB4, CD80 and cytokines, complement, and clusterin (CLU) that binds to misfolded proteins. In contrast, arrested highly infectious CJ+ cells (10 logs/gm) downregulated many replication controls. Furthermore, arrested CJ+ cells suppressed neuronal differentiation transcripts, including Prnp which is essential for CJ agent infection. CJ+ cells also enhanced IFN stimulated pathways, and analysis of the 342 CJ+ unique transcripts revealed additional innate immune and anti-viral-linked transcripts, e.g., Il17, ISG15, and RSAD2 (viperin). These data show: 1) innate immune transcripts are produced by normal neurons during differentiation; 2) CJ infection can enhance and expand anti-viral responses; 3) latent CJ infection epigenetically imprints many proliferative pathways to thwart complete arrest. CJ+ brain microglia, white blood cells and intestinal myeloid cells with shared transcripts may be stimulated to educe latent CJD infections that can be clinically silent for >30 years.

Oriented surface imprinting of epitopes anchored on silica nanoparticles containing quantum dots by thiol-disulfide exchange reactions for the enhanced fluorescence detection of proteins.

As artificial receptors for protein recognition, epitope-imprinted polymers combined with fluorescence sensing based on quantum dots (QDs) can be potentially used for biological analysis and disease diagnosis. However, the usual way for fabrication of QD sensors through unoriented epitope imprinting is confronted with the problems of disordered imprinting sites and low template utilization. In this context, a facile and efficient oriented epitope surface imprinting was put forward based on immobilization of the epitope templates via thiol-disulfide exchange reactions. With N-succinimidyl 3-(2-pyridyldithio)-propionate (SPDP) as a heterobifunctional reagent, cysteine-modified epitopes of cytochrome c were anchored on the surface of pyridyl disulfide functionalized silica nanoparticles sandwiching CdTe QDs. After surface imprinting via a sol-gel process, the epitope templates were removed from the surface-imprinted layers simply by reduction of the thiol-disulfide, affording oriented epitope-imprinted sites. By this method, the amount of epitope templates was only 1/20 of traditionally unoriented epitopes. The resulting sensors demonstrated significantly enhanced imprinting performance and high sensitivity, with the imprinting factor increasing from 2.6 to 3.9, and the limit of detection being 91 nM. Such epitope-oriented surface-imprinted method may offer a new design strategy for the construction of high-affinity protein recognition nanomaterials with fluorescence sensing.

Finite immune imprinting on neutralizing antibody responses to Omicron subvariants by repeated vaccinations.

OBJECTIVE: To investigate the effects of repeated vaccination with ancestral SARS-CoV-2 (Wuhan-hu-1)-based inactivated, recombinant protein subunit or vector-based vaccines on the neutralizing antibody response to Omicron subvariants. METHODS: Individuals who received four-dose vaccinations with the Wuhan-hu-1 strain, individuals who were infected with the BA.5 variant alone without prior vaccination, and individuals who experienced a BA.5 breakthrough infection following receiving 2-4 doses of the Wuhan-hu-1 vaccine were enrolled. Neutralizing antibodies against D614G, BA.5, XBB.1.5, EG.5.1, and BA.2.86 were detected using a pseudovirus-based neutralization assay. Antigenic cartography was used to analyze cross-reactivity patterns among D614G, BA.5, XBB.1.5, EG.5.1, and BA.2.86 and sera from individuals. RESULTS: The highest neutralizing antibody titers against D614G were observed in individuals who only received four-dose vaccination and those who experienced BA.5 breakthrough infection, which was also significantly higher than the antibody titers against XBB.1.5, EG.5.1, and BA.2.86. In contrast, only BA.5 infection elicited comparable neutralizing antibody titers against the tested variants. While neutralizing antibody titers against D614G or BA.5 were similar across the cohorts, the neutralizing capacity of antibodies against XBB.1.5, EG.5.1, and BA.2.86 was significantly reduced. BA.5 breakthrough infection following heterologous booster induced significantly higher neutralizing antibody titers against the variants, particularly against XBB.1.5 and EG.5.1, than uninfected vaccinated individuals, only BA.5 infected individuals, or those with BA.5 breakthrough infection after primary vaccination. CONCLUSIONS: Our findings suggest that repeated vaccination with the Wuhan-hu-1 strain imprinted a neutralizing antibody response toward the Wuhan-hu-1 strain with limited effects on the antibody response to the Omicron subvariants.

Fundamentals, Synthetic Strategies and Applications of Non-Covalently Imprinted Polymers.

Molecular imprinting has emerged as an important and practical technology to create economical and stable synthetic mimics of antibodies and enzymes. It has already found a variety of important applications, such as affinity separation, chemical/biological sensing, disease diagnostics, proteomics, bioimaging, controlled drug release, and catalysis. In the past decade, significant breakthroughs have been made in non-covalently imprinted polymers, from their synthesis through to their applications. In terms of synthesis, quite a few versatile and facile imprinting approaches for preparing MIPs have been invented, which have effectively solved some key issues in molecular imprinting. Additionally, important applications in several areas, such as sensors, proteomics and bioimaging, have been well demonstrated. In this review, we critically and comprehensively survey key recent advances made in the preparation of non-covalently imprinted polymers and their important applications. We focus on the state-of-art of this technology from three different perspectives: fundamentals, synthetic strategies, and applications. We first provide a fundamental basis for molecular imprinting technologies that have been developed, which is extremely helpful for establishing a sound understanding of the challenges in molecular imprinting. Then, we discuss in particular the major breakthroughs within the last ten years (2014-2024), with emphasis on new imprinting approaches, what strengths the breakthroughs can provide, and which new applications the properties of the prepared non-covalently imprinted polymers are fit for.

Self-Cleaning Hydrophobic Coating Composed of Micro/Nano-Imprinted Polydimethylsiloxane with Enhanced Light In-Coupling Capabilities.

In this study, we have optimized optically transparent polydimethylsiloxane (PDMS) hydrophobic coating on glass substrates that exhibit self-cleaning as well as enhanced light in-coupling capabilities. Micro/nano textures on the surface of PDMS were introduced through micro/nanoimprinting to achieve light trapping as well as self-cleaning abilities. Comprehensive studies show that the periodic arrangement of the micro/nanopatterned features has enabled enhanced inward transmission of light in the visible range along with superior hydrophobicity. The water contact angle (WCA) measurements on these coatings demonstrated a superior capacity for self-cleaning with a WCA of about 117°. Subsequently, when these transparent and hydrophobic coatings were deposited on commercial silicon solar cells, they showed a 15.8% increment in efficiency due to enhanced light in-coupling with a nanopatterned PDMS coating.

Hybrid immunity to SARS-CoV-2 arises from serological recall of IgG antibodies distinctly imprinted by infection or vaccination.

We describe the molecular-level composition of polyclonal immunoglobulin G (IgG) anti-spike antibodies from ancestral severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, vaccination, or their combination ("hybrid immunity") at monoclonal resolution. Infection primarily triggers S2/N-terminal domain (NTD)-reactive antibodies, whereas vaccination mainly induces anti-receptor-binding domain (RBD) antibodies. This imprint persists after secondary exposures wherein >60% of ensuing hybrid immunity derives from the original IgG pool. Monoclonal constituents of the original IgG pool can increase breadth, affinity, and prevalence upon secondary exposures, as exemplified by the plasma antibody SC27. Following a breakthrough infection, vaccine-induced SC27 gained neutralization breadth and potency against SARS-CoV-2 variants and zoonotic viruses (half-maximal inhibitory concentration [IC50] ∼0.1-1.75 nM) and increased its binding affinity to the protective RBD class 1/4 epitope (dissociation constant [KD] < 5 pM). According to polyclonal escape analysis, SC27-like binding patterns are common in SARS-CoV-2 hybrid immunity. Our findings provide a detailed molecular definition of immunological imprinting and show that vaccination can produce class 1/4 (SC27-like) IgG antibodies circulating in the blood.

RhizoMAP: a comprehensive, nondestructive, and sensitive platform for metabolic imaging of the rhizosphere.

BACKGROUND: Elucidating the intricate structural organization and spatial gradients of biomolecular composition within the rhizosphere is critical to understanding important biogeochemical processes, which include the mechanisms of root-microbe interactions for maintaining sustainable plant ecosystem services. While various analytical methods have been developed to assess the spatial heterogeneity within the rhizosphere, a comprehensive view of the fine distribution of metabolites within the root-soil interface has remained a significant challenge. This is primarily due to the difficulty of maintaining the original spatial organization during sample preparation without compromising its molecular content. RESULTS: In this study, we present a novel approach, RhizoMAP, in which the rhizosphere molecules are imprinted on selected polymer membranes and then spatially profiled using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI). We enhanced the performance of RhizoMAP by combining the use of two thin (< 20 µm) membranes (polyester and polycarbonate) with distinct MALDI sample preparations. This optimization allowed us to gain insight into the distribution of over 500 different molecules within the rhizosphere of poplar (Populus trichocarpa) grown in rhizoboxes filled with mycorrhizae soil. These two membranes, coupled with three different sample preparation conditions, enabled us to capture the distribution of a wide variety of molecules that included phytohormones, amino acids, sugars, sugar glycosides, polycarboxylic acids components of the Krebs cycle, fatty acids, short aldehydes and ketones, terpenes, volatile organic compounds, fertilizers from the soil, and others. Their spatial distribution varies greatly, with some following root traces, others showing diffusion from roots, some associated with soil particles, and many having distinct hot spots along the plant root or surrounding soil. Moreover, we showed how RhizoMAP can be used to localize the origin of the molecules and molecular transformation during root growth. Finally, we demonstrated the power of RhizoMAP to capture molecular distributions of key metabolites throughout a 20 cm deep rhizosphere. CONCLUSIONS: RhizoMAP is a method that provides nondestructive, untargeted, broad, and sensitive metabolite imaging of root-associated molecules, exudates, and soil organic matter throughout the rhizosphere, as demonstrated in a lab-controlled native soil environment.

Immunity against conserved epitopes dominates after two consecutive exposures to SARS-CoV-2 Omicron BA.1.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exposure histories become increasingly complex through original and variant-adapted vaccines and infections with viral variants. Upon exposure to the highly altered Omicron spike glycoprotein, pre-immunized individuals predominantly mount recall responses of Wuhan-Hu-1 (wild-type)-imprinted memory B (BMEM) cells mostly targeting conserved non-neutralizing epitopes, leading to diminished Omicron neutralization. We investigated the impact of imprinting in individuals double/triple vaccinated with a wild-type-strain-based mRNA vaccine who, thereafter, had two consecutive exposures to Omicron BA.1 spike (breakthrough infection followed by BA.1-adapted vaccine). We found that depletion of conserved epitope-recognizing antibodies using a wild-type spike bait results in strongly diminished BA.1 neutralization. Furthermore, spike-specific BMEM cells recognizing conserved epitopes are much more prevalent than BA.1-specific BMEM cells. Our observations suggest that imprinted BMEM cell recall responses limit the induction of strain-specific responses even after two consecutive BA.1 spike exposures. Vaccine adaptation strategies need to consider that prior SARS-CoV-2 infections and vaccinations may cause persistent immune imprinting.

Multi-locus imprinting disturbance (MLID): interim joint statement for clinical and molecular diagnosis.

BACKGROUND: Imprinting disorders are rare diseases resulting from altered expression of imprinted genes, which exhibit parent-of-origin-specific expression patterns regulated through differential DNA methylation. A subgroup of patients with imprinting disorders have DNA methylation changes at multiple imprinted loci, a condition referred to as multi-locus imprinting disturbance (MLID). MLID is recognised in most but not all imprinting disorders and is also found in individuals with atypical clinical features; the presence of MLID often alters the management or prognosis of the affected person. Some cases of MLID are caused by trans-acting genetic variants, frequently not in the patients but their mothers, which have counselling implications. There is currently no consensus on the definition of MLID, clinical indications prompting testing, molecular procedures and methods for epigenetic and genetic diagnosis, recommendations for laboratory reporting, considerations for counselling, and implications for prognosis and management. The purpose of this study is thus to cover this unmet need. METHODS: A comprehensive literature search was conducted resulting in identification of more than 100 articles which formed the basis of discussions by two working groups focusing on clinical diagnosis (n = 12 members) and molecular testing (n = 19 members). Following eight months of preparations and regular online discussions, the experts from 11 countries compiled the preliminary documentation and determined the questions to be addressed during a face-to-face meeting which was held with the attendance of the experts together with four representatives of patient advocacy organisations. RESULTS: In light of available evidence and expert consensus, we formulated 16 propositions and 8 recommendations as interim guidance for the clinical and molecular diagnosis of MLID. CONCLUSIONS: MLID is a molecular designation, and for patients with MLID and atypical phenotypes, we propose the alternative term multi-locus imprinting syndrome. Due to the intrinsic variability of MLID, the guidelines underscore the importance of involving experts from various fields to ensure a confident approach to diagnosis, counselling, and care. The authors advocate for global, collaborative efforts in both basic and translational research to tackle numerous crucial questions that currently lack answers, and suggest reconvening within the next 3-5 years to evaluate the research advancements and update this guidance as needed.

Parent of origin genetic effects on milk production traits in a population of Iranian Holstein cows.

The aim was to estimate the relative contribution of imprinting effects from both paternal and maternal sides to phenotypic variation in milk production traits including 305 days milk yield (MY), average daily milk production (ADM), fat percentage (F%), protein percentage (P%), 305 days fat yield (FY), 305 days protein yield (PY), ratio of fat percentage to protein percentage (F:P) and somatic cell score (SCS) in Iranian Holstein cows. To do this, each trait was analysed with a series of four animal models, which were identical for fixed and additive genetic effects but differed for combinations of paternal and maternal imprinting effects. The log-likelihood ratio test (LRT) and Akaike's information criteria (AIC) were used to select the best model for each trait. Correlations between traits due to additive and imprinting effects were estimated by bivariate analyses. For all traits studied, fitting the imprinting effect led to a better data fit. Also, it resulted in a noticeable decrease in additive genetic variance from 8% (SCS) to 28% (F:P). A significant maternal imprinting effect was detected on all traits studied. Estimates of maternal imprinting heritability ( h mi 2 $$ {h}_{\mathrm{mi}}^2 $$ ) were 0.07 ± 0.02, 0.04 ± 0.01, 0.06 ± 0.01, 0.05 ± 0.01, 0.5 ± 0.01, 0.09 ± 0.02, 0.07 ± 0.02 and 0.06 ± 0.01 for MY, ADM, F%, P%, FY, PY, F:P and SCS, respectively. For F:P, in addition to the maternal imprinting effect, a significant paternal imprinting component was also detected with a 7% contribution to phenotypic variance of F:P. Estimates of direct heritability ( h a 2 $$ {h}_{\mathrm{a}}^2 $$ ) were 0.29 ± 0.02, 0.17 ± 0.01, 0.22 ± 0.02, 0.11 ± 0.01, 0.18 ± 0.02, 0.22 ± 0.02, 0.15 ± 0.04 and 0.06 ± 0.01 for MY, ADM, F%, P%, FY, PY, F:P and SCS, respectively. Maternal imprinting correlations (rmi) were in a wide range between -0.75 ± 0.15 (P%-SCS) and 0.95 ± 0.11 (MY-ADM). Additive genetic correlations (ra) ranged between -0.54 ± 0.05 (MY-P%) and 0.99 ± 0.01 (MY-ADM) and phenotypic correlations (rp) ranged from -0.30 ± 0.01 (MY-F%) to 0.93 ± 0.01 (MY-ADM). The Spearman's correlation between additive breeding values including and excluding imprinting effects deviated from unity especially for top-ranked animals implying re-ranking of top animals following the inclusion of imprinting effects in the model. Since including imprinting effects in the model resulted in better data fit and re-ranking of top animals, including these effects in the genetic evaluation models for milk production traits was recommended.

Design of pH-responsive molecularly imprinted polymer as a carrier for controlled and sustainable capecitabine release.

A molecularly imprinting polymer (MIP) carrier with pH-responsivity was designed to construct a drug delivery system (DDS) focusing on controlled and sustainable capecitabine (CAPE) release. The pH-responsive characteristic was achieved by the functionalization of SiO2 substrate with 4-formylphenylboronic acid, accompanied by the introduction of fluorescein isothiocyanate for the visualization of the intracellular localization of the nanocarrier. Experimental results indicated that CAPE was adsorbed onto the drug carrier with satisfactory encapsulation efficiency. The controlled release of CAPE was realized based on the break of borate ester bonds between -B(OH)2 and cis-diols in the weakly acidic environment. Density functional theory computations were conducted to investigate the adsorption/release mechanism. Moreover, in vitro experiments confirmed the good biocompatibility and ideal inhibition efficiency of the developed DDS. The MIP can act as an eligible carrier and exhibits the great potential in practical applications for tumor treatment.

Antimicrobial assay and controlled drug release studies with novel eugenol imprinted p(HEMA)-bacterial cellulose nanocomposite, designed for biomedical applications.

In this study, a novel bio-composite material that allow sustained release of plant derived antimicrobial compound was developed for the biomedical applications to prevent the infections caused by microorganisms resistant to commercial antimicrobials agents. With this aim, bacterial cellulose (BC)-p(HEMA) nanocomposite film that imprinted with eugenol (EU) via metal chelated monomer, MAH was prepared. Firstly, characterization studies were utilized by FTIR, SEM and BET analysis. Then antimicrobial assays, drug release studies and in vitro cytotoxicity test were performed. A significant antimicrobial effect against both Gram (+) Staphylococcus aureus and Gram (-) Escherichia coli bacteria and a yeast Candida albicans were observed even in low exposure time periods. When antimicrobial effect of EU compared with commercially used agents, both antifungal and antibacterial activity of EU were found to be higher. Then, sustained drug release studies showed that approximately 55% of EU was released up to 50 h. This result proved the achievement of the molecular imprinting for an immobilization of molecules that desired to release on an area in a long-time interval. Finally, the in vitro cytotoxicity experiment performed with the mouse L929 cell line determined that the synthesized EU-imprinted BC nanocomposite was biocompatible.

Fetus Conceived via In Vitro Fertilization With Mosaic Uniparental Isodisomy and Two Balanced Translocations.

We present a case of a fetus acquiring two different balanced translocations from each parent and subsequent uniparental isodisomy from postzygotic loss of a paternal chromosome. Balanced chromosomal translocations occur in 0.14% of the population and increase the risk of other genetic abnormalities, such as uniparental disomy (UPD) and mosaicism. Preimplantation genetic testing (PGT) can identify some genetic abnormalities. Translocations t(6;21) and t(5;15) have been reported individually but never together in a viable fetus. A non-consanguineous couple who were known carriers of two different balanced translocations conceived via classic in vitro fertilization (IVF). They had a normal PGT completed. Chorionic villus sampling (CVS) revealed that the fetus had received t(6;21) from the mother and t(5;15) from the father. The probability of the fetus acquiring both translocations was 2.8%. CVS also revealed UPD of chromosome 14. Amniocentesis was performed, which was consistent with the CVS in detecting the balanced translocations but provided more information about the UPD, determining that it was a mosaic maternal uniparental isodisomy of chromosome 14 (UPD(14)mat). The couple underwent genetic counseling to discuss the above findings and ultimately decided on dilation and evacuation at 17 weeks of gestation. The likelihood of conception of this fetus and survival past the first trimester is extremely rare. These specific chromosomal translocations and (UPD(14)mat) have never been reported before. This case emphasizes the concomitant nature of imprinted genes, resulting in multiple genetically unique alterations. This report also highlights the limitations of PGT, CVS, and amniocentesis in being reproducibly consistent, which is important to discuss prior to IVF conception.

Dual-template magnetic molecularly imprinted polymers for selective extraction and sensitive detection of aflatoxin B1 and benzo(α)pyrene in environmental water and edible oil.

The coexistence of multiple contaminates in the environment and food is of growing concern due to their extremely hazard as a well-known class I carcinogen, like aflatoxin B1 (AFB1) and benzo(α)pyrene (BaP). AFB1 and BaP are susceptible to coexistence in environmental water and edible oil, posing a significant potential risk to environmental monitoring and food safety. The remaining challenges in detecting multiple contaminates include unsatisfied sensitivity, insufficient targets selectivity, and interferences in complex matrices. Here, we developed dual-template magnetic molecularly imprinted polymers (DMMIPs) for selective extraction of dual targets in complex matrices from the environment and food. The DMMIPs were fabricated by surface imprinting with vinyl-functionalized Fe3O4 as carrier, 5,7-dimethoxycoumarin and pyrene as dummy templates, and methacrylamide as functional monomer. The DMMIPs showed excellent adsorption ability (12.73-15.80 mg/g), imprinting factors (2.01-2.58), and reusability of three adsorption-desorption cycles for AFB1 and BaP. The adsorption mechanism including hydrogen bond, electrostatic interaction and van der Waals force was confirmed by physical characterization and DFT calculation. Applying DMMIPs in magnetic solid phase extraction (MSPE) followed by high-performance liquid chromatography (HPLC) analysis enabled detection limits of 0.134 µg/L for AFB1 and 0.107 µg/L for BaP. Recovery rates for water and edible oil samples were recorded as 86.2%-110.3% with RSDs of 4.1%-11.9%. This approach demonstrates potential for simultaneous identification and extraction of multiple contaminants in environmental and food.

Facile biotic/abiotic sandwich detection system for the highly sensitive detection of human serum albumin and glycated albumin.

Quantifying glycated albumin (GA) levels in the blood is crucial for diagnosing diabetes because they strongly correlate with blood glucose concentration. In this study, a biotic/abiotic sandwich assay was developed for the facile, rapid, and susceptible detection of human serum albumin (HSA) and GA. The proposed sandwich detection system was assembled using a combination of two synthetic polymer receptors and natural antibodies. Molecularly imprinted polymer nanogels (MIP-NGs) for HSA (HSA-MIP-NGs) were used to mimic capture antibodies, whereas antibodies for HSA or GA were used as primary antibodies and fluorescent signaling MIP-NGs for the Fc domain of IgG (F-Fc-MIP-NGs) were used as a secondary antibody mimic to indicate the binding events. The HSA/anti-HSA/F-Fc-MIP-NGs complex, formed by incubating HSA and anti-HSA antibodies with F-Fc-MIP-NGs, was captured by HSA-MIP-NGs immobilized on the chips for fluorescence measurements. The analysis time was less than 30 min, and the limit of detection was 15 pM. After changing the anti-HSA to anti-GA (monoclonal antibody), the fluorescence response toward GA exceeded that of HSA, indicating successful GA detection using the proposed sandwich detection system. Therefore, the proposed system could change the detection property by changing a primary antibody, indicating that this system can be applied to various target proteins and, especially, be a powerful approach for facile and rapid analysis methods for proteins with structural similarity.

Nanoparticles that Distinguish Chemical and Supramolecular Contexts of Lysine for Single-Site Functionalization of Protein.

Lysine is one of the most abundant residues on the surface of proteins and its site-selective functionalization is extremely challenging. The existing methods of functionalization rely on differential reactivities of lysine on a protein, making it impossible to label less reactive lysines selectively. We here report polymeric nanoparticles that mimic enzymes involved in the posttranslational modifications of proteins that distinguish the chemical and supramolecular contexts of a lysine and deliver the labeling reagent precisely to its ε amino group. The nanoparticles are prepared through molecular imprinting of cross-linkable surfactant micelles, plus an in situ, on-micelle derivatization of the peptide template prior to the imprinting. The procedures encode the polymeric nanoparticles with all the supramolecular information needed for sequence identification and precise labeling, allowing single-site functionalization of a predetermined lysine on the target protein in a mixture.

Protocol for DNA Methylation Editing of Imprinted Loci and Assessment of the Effects.

In this chapter, we present an experimental protocol to conduct DNA methylation editing experiments, that is, to induce loss or gain of DNA methylation, targeting Dlk1-Dio3 imprinted domain, a well-studied imprinted locus, in ES cells. In this protocol, plasmid vectors expressing the DNA methylation editing tools, combining the CRISPR/dCas9 system and the SunTag system coupled to a DNA methyltransferase or a TET enzyme, are introduced into cells for transient expression. By employing this strategy, researchers can effectively investigate a distinct DNA methylation signature that has an impact on the imprinting status, including gene expression and histone modifications, across the entire domain. We also describe strategies for allele-specific quantitative analyses of DNA methylation, gene expression, and histone modifications and binding protein levels for assessing the imprinting state of the locus.

Protocol for Allele-Specific Epigenome Editing Using CRISPR/dCas9.

The discovery and adaptation of CRISPR/Cas systema for epigenome editing has allowed for a straightforward design of targeting modules that can direct epigenome editors to virtually any genomic site. This advancement in DNA-targeting technology brings allele-specific epigenome editing into reach, a "super-specific" variation of epigenome editing whose goal is an alteration of chromatin marks at only one selected allele of the genomic target locus. This technology could be useful for the treatment of diseases caused by a mutant allele with a dominant effect, because allele-specific epigenome editing allows the specific silencing of the mutated allele leaving the healthy counterpart expressed. Moreover, it may allow the direct correction of aberrant imprints in imprinting disorders where editing of DNA methylation is required exclusively in a single allele. Here, we describe a basic protocol for the design and application of allele-specific epigenome editing systems using allele-specific DNA methylation at the NARF gene in HEK293 cells as an example. An sgRNA/dCas9 unit is used for allele-specific binding to the target locus containing a SNP in the seed region of the sgRNA or the PAM region. The dCas9 protein is connected to a SunTag allowing to recruit up to 10 DNMT3A/3L units fused to a single-chain Fv fragment, which specifically binds to the SunTag peptide sequence. The plasmids expressing dCas9-10x SunTag, scFv-DNMT3A/3L, and sgRNA, each of them co-expressing a fluorophore, are introduced into cells by co-transfection. Cells containing all three plasmids are enriched by FACS, cultivated, and later the genomic DNA and RNA can be retrieved for DNA methylation and gene expression analysis.