Effect of Modification Strategies on the Biological Activity of Peptides/Proteins.

Covalent attachment of biologically active peptides/proteins with functional moieties is an effective strategy to control their biodistribution, pharmacokinetics, enzymatic digestion, and toxicity. This review focuses on the characteristics of different modification strategies and their effects on the biological activity of peptides/proteins and illustrates their relevant applications and potential.

Effect of Mini-PEGs Modification on the Enzymatic Digestion of D-Amino Acid-Containing Peptides under the Action of PROK.

It was previously reported that D-amino acid-containing peptides exhibited the ability to resist enzymatic hydrolysis. This study investigated the influence of mini-PEGs modification on enzymatic hydrolysis ability of D-amino acid-containing peptides. The results showed that PEGylation promoted enzymatic hydrolysis of the D-amino acid-containing peptide, especially, the cleavage rate of the D-amino acid-containing peptide 6-w with PEG3 modification at the N-ends was up to 17 times higher in the presence of proteinase K (PROK) compared to those without PEG3 modification. Moreover, analysis of the enzymatic cleavage sites demonstrated a similar cleavage pattern of the PEGylated D-amino acid-containing peptide to that of the unmodified peptide. The computational simulations further showed that the enhanced enzymatic hydrolysis ability can be attributed to the strong interaction between PROK and the peptide after PEG3 modification and the resulting formation of a mature catalytic triad structure.

Self-Assembly Nanostructure Induced by Regulation of G-Quadruplex DNA Topology via a Reduction-Sensitive Azobenzene Ligand on Cells.

The control of DNA assembly systems on cells has increasingly shown great importance for precisely targeted therapies. Here, we report a controllable DNA self-assembly system based on the regulation of G-quadruplex DNA topology by a reduction-sensitive azobenzene ligand. Specifically, three azobenzene multiamines are developed, and AzoDiTren is identified as the best G4 binder, which displays high affinity and specificity for G4 DNA. Moreover, the reduction-sensitive nature of the azobenzene scaffold allows AzoDiTren to induce a complete change of the G4 topology in a tissue-specific manner, even at high metal cation concentrations. On this basis, the AzoDiTren-induced G4 conformational switch achieves control of the self-assembly of G4-functionalized DNAs on cells. This strategy enables the regulation of G4 and DNA self-assembly by the bioreductant-responsive ligand.

Association of Different Total Bilirubin Levels with Prognosis of Peritoneal Dialysis-Associated Peritonitis.

Background and Objectives: Peritoneal dialysis-associated peritonitis (PDAP) poses significant challenges in peritoneal dialysis (PD) patient management and outcomes. Total bilirubin has gained attention due to its antioxidant and immunomodulatory properties. However, its relationship with PDAP prognosis remains underexplored. Materials and Methods: We conducted a retrospective single-center study involving 243 PDAP patients stratified into tertile-based groups according to total bilirubin levels. The association between total bilirubin levels and treatment failure risk was investigated through statistical analyses and restricted cubic spline curve analysis. Results: Our analysis revealed a non-linear correlation between total bilirubin levels and PDAP treatment failure risk. At total bilirubin levels below 8.24 µmol/L, a protective effect was observed, while levels exceeding this threshold heightened the risk of treatment failure. Conclusions: This study unveils a dual role of total bilirubin in PDAP prognosis. Below a certain threshold, it confers protection, while higher levels exacerbate the risk of treatment failure. These findings emphasize the need for further investigation in larger, multicenter prospective studies to validate and elucidate the mechanisms behind bilirubin's impact on PDAP, potentially guiding the development of targeted therapeutic strategies.

Reversible On-Off Photoswitching of DNA Replication Using a Dumbbell Oligodeoxynucleotide.

In most organisms, DNA extension is highly regulated; however, most studies have focused on controlling the initiation of replication, and few have been done to control the regulation of DNA extension. In this study, we adopted a new strategy for azODNs to regulate DNA extension, which is based on azobenzene oligonucleotide chimeras regulated by substrate binding affinity, and the conformation of the chimera can be regulated by a light source with a light wavelength of 365 nm. The results showed that the primer was extended with Taq DNA polymerase after visible light treatment, and DNA extension could be effectively hindered with UV light treatment. We also verify the reversibility of the photoregulation of primer extension through photoswitching of dumbbell asODNs by alternate irradiation with UV and visible light. Our method has the advantages of fast and simple, green response and reversible operations, providing a new strategy for regulating gene replication.

A ratiometric nanoprobe based on carboxylated graphitic carbon nitride nanosheets and Eu3+ for the detection of tetracyclines.

A ratiometric fluorescence method based on carboxylated graphitic carbon nitride nanosheets (C-g-C3N4) and Eu3+ (C-g-C3N4-Eu3+) is described for the detection of tetracyclines (TCs), a broad-spectrum antibiotic. C-g-C3N4, which was used as a fluorescence enhancer of Eu3+, was prepared by direct pyrolysis of melamine and post-functionalization. In the presence of TCs, the fluorescence intensity of Eu3+ at 616 nm increased, accompanied by a decrease of fluorescence intensity of C-g-C3N4 at 435 nm. Under the optimal conditions, the ratio of fluorescence intensity at 616 nm to the one at 435 nm (I616/I415) increases linearly in the 10 nM to 40 µM TC concentration range with a detection limit of 7.7 nM (S/N = 3). It has been successfully applied in the detection of TCs in spiked tap water and soil samples with satisfactory recovery (96.6-107.2%) and high precision. Furthermore, a test paper and smartphone can assist in rapidly detecting TCs due to the emission color change from blue to red with the addition of TCs. This shows that the proposed method has great potential for the rapid detection TCs in real samples.

Simultaneous determination of the herbicide bixlozone and its metabolites in plant and animal samples by liquid chromatography-tandem mass spectrometry.

Tracing the herbicide bixlozone and its metabolites in food is necessary to assess their risks to human health. In the study, a rapid and effective analytical method using the quick, easy, cheap, effective, rugged, and safe method for the simultaneous determination of bixlozone and its metabolites (2,4-dichlorobenzoic acid, 3-hydroxy-propanamide-bixlozone, and 5'-hydroxy-bixlozone) in plant and animal samples (tomato, cucumber, apple, wheat flour, meat, milk, and egg) was developed based on ultra high performance liquid chromatography-tandem mass spectrometry. The method was validated based on the linearity (R2  > 0.99), sensitivity (limit of quantification = 0.01 mg/kg), recovery (70.2-115.1%), and precision (intraday 1.2-17.6%, interday 0.3-16.0%). Detection was achieved within 6.0 min. The method is reliable for the determination of four target compounds in all seven matrices. The satisfactory validation criteria and successful application show that the proposed methodology is suitable for the detection of four target compounds in real matrices.

Metallic Fingerprints of Carbon: Label-Free Tracking and Imaging of Graphene in Plants.

Detection and quantification of carbon nanomaterials are extremely challenging, especially under the background interference of carbon. Here, we propose a new label-free method to quantify, track, and in situ image graphene and graphene oxide (GO) in plants based on their inherent metallic impurities as fingerprints. We show the ubiquity and high stability of inherent metallic fingerprints of graphene and GO obtained from different exposure routes under the natural environments, which enables the materials to be easily quantified and in situ imaged by high-sensitivity (laser ablation) inductively coupled plasma mass spectrometry. The method was applied to investigate the uptake and spatial distribution of graphene and GO in soybean plants. The plants were cultivated in graphene or GO solutions for 7 days, and the indicative elements (Ni or Mn) in different parts of plants were monitored and imaged. We found that graphene and GO showed different distribution patterns in plants (the highest uptake percentages in root up to 14.4% for graphene and 47.8% for GO), and high concentration of material exposure might cause excessive accumulation of materials in roots which blocked their further transport to the other parts of plants. The present method is more straightforward, accessible, and economical than normally used isotopic or metal-labeling methods. It also avoids the uncertainties or alterations of properties caused by the labeling process and thus has great promise in analysis and risk assessment of carbon nanomaterials.

Replication of DNA Containing Mirror-Image Thymidine in E. coli Cells.

DNA damage can occur naturally or through environmental factors, leading to mutations in DNA replication and genomic instability in cells. Normally, natural d-nucleotides were selected by DNA polymerases. The template l-thymidine (l-T) has been shown to be bypassed by several types of DNA polymerases. However, DNA replication fidelity of nucleotide incorporation opposite l-thymidine in vivo remains unknown. Here, we constructed plasmids containing a restriction enzyme (PstI) recognition site in which the l-T lesion was site-specifically located within the PstI recognition sequence (CTGCAG). Further, we assessed the efficiencies of nucleotide incorporation opposite the l-T site and l-T lesion bypass replication in vitro and in vivo. We found that recombinants containing the l-T lesion site inhibited DNA replication. In addition, A was incorporated opposite the l-T lesion by routine PCR assay, whereas preference for nucleotide incorporation opposite the l-T site was A (13%), T (22%), C (46%), and G (19%), and no nucleotide insertion and deletions were detected in E. coli cells. In particular, a novel restriction enzyme-mediated method for detection of the mutagenic properties of DNA lesion was established, which allows us to readily detect restriction-digestion of the l-T-bearing plasmids. The study provided significant insight into how mirror-image nucleosides perturb the fidelity of DNA replication in vivo and whether they elicit mutagenic effects, which may help to understand both how DNA damage interferes with the flow of genetic information during DNA replication and development of diseases caused by gene mutation.

New insight into enzymatic hydrolysis of peptides with site-specific amino acid d-isomerization.

The isomerization of l-amino acids in peptides and proteins into d-configuration under physiological conditions would affect the physiological dysfunction and caused protein conformational diseases. The presence of d-amino acids might change the higher-order structure of proteins and triggered abnormal aggregation. In order to better understand this phenomenon and promote degradation, we systematically studied the enzymatic hydrolysis of a series of peptides obtained by replacing l-amino acids in different positions of template peptide KYNETWRSED with d-amino acids under the action of Protease K. The results showed that, compared with normal peptide, isomerization of different amino acids had different effects on the anti-enzymatic hydrolysis of the peptides, especially d-tryptophan at position 6, which significantly inhibited enzymatic hydrolysis. The analysis of the peptide cleavage site revealed that the efficiency of enzymatic hydrolysis mainly depended on the isomerization of the amino acids at a specific site of the peptide cleavage. Further studies showed that the enzymatic hydrolysis of substrates could be facilitated by optimized reaction conditions such as temperature, pH, addition of metal ions, and change of buffer. In this way the accumulation of disease-associated d-amino acid containing polypeptides/proteins could be prevented.

Direct Mass Spectrometry Analysis Using In-Capillary Dicationic Ionic Liquid-Based in Situ Dispersive Liquid-Liquid Microextraction and Sonic-Spray Ionization.

The current study reports on a direct mass spectrometry (MS) analysis method using in-capillary dicationic ionic liquid (DIL)-based in situ dispersive liquid-liquid microextraction (DLLME) and sonic-spray ionization (SSI). The developed method merged extraction, enrichment, ionization, and detection of perfluorinated compounds (PFCs) in environmental water into a single step. A microliter-scale ternary fluidic system was designed and integrated into a disposable pulled capillary, in which an imidazolium-based germinal DIL reagent activated an in situ metathesis reaction. A penetrating slug-flow microextraction (SFME) process was subsequently initiated with significantly enhanced interfacial areas and mass transfer rates for the analytes of interest, the mechanism of which was revealed by simulations. An SSI assembly was in-house built, and it enabled a Venturi self-pumping using a stream of nitrogen gas flow coaxial to the capillary under atmospheric pressure to automatically spray at the tip of the capillary. The in situ formed DIL could bind with anionic PFC analytes to generate a positively charged complex, which benefits a signal increase of 1 to 2 orders in magnitude in the positive ion mode than in the negative ion mode for most analytes. The high sensitivity allowed the measure of sub-ppb (parts per billion) levels of PFCs in the environmental water samples. The developed method is a promising protocol for MS analysis because of unprecedented ease, significantly enhanced sensitivity, and potentially high sample throughput.

Reversible Photocontrol of Thrombin Activity by Replacing Loops of Thrombin Binding Aptamer using Azobenzene Derivatives.

The photoisomerization of azobenzenes provides a general means for the photocontrol of many important biomolecular structures and organismal functions. For temporal and spatial control activity of thrombin binding aptamer (TBA) by light, azobenzene derivatives were carefully selected as light-triggered molecular switches to replace TT loops and the TGT loop of TBA to reversibly control enzyme activity. These molecules interconverted between the trans and cis states under alternate UV and visible light irradiation, which consequently triggered reversible formation of G-quadruplex morphology. In addition, we investigated the impact of three azobenzene derivatives on stability, thrombin binding ability, and anticoagulant properties. The result showed that 4,4'-bis(hydroxymethyl)azobenzene at the TGT loop position significantly photoregulated affinity to thrombin and blood clotting in human plasma, which provided a successful strategy to control blood clotting in human plasma and a further evidence for design of TBA analogues with pivotal positions of modifications.

Bioactivatable reductive cleavage of azobenzene for controlling functional dumbbell oligodeoxynucleotides.

Application of stimuli-responsive bioactive molecules is an attractive strategy due to use for target special tissues and cells. Here, we reported synthesis of an azo-linker, 2,2'-dimethoxyl-4,4'-dihydroxymethylazobenzene (mAzo), which was more effectively recognized and cleaved by reducing glutathione (GSH) via comparing with 4,4'-dihydroxymethylazobenzene (Azo). In addition, mAzo is further exploited to engineer dumbbell asODNs, which could result in the release of asODNs and thus modulate their hybridization to target nucleic acids. The present study is the first example to disclose efficient reductive cleavage of azobenzene by GSH to generate aromatic amine. This would provide a valuable strategy for tunable cell-specific release of ODNs and modulation of known disease-causing gene expression in cancer cells.

Preparation of hierarchically porous carbon from cellulose as highly efficient adsorbent for the removal of organic dyes from aqueous solutions.

The hierarchically porous carbons were prepared from cellulose by a one-step method and studied as dye-adsorbents using chrysoidine as a model. With the increase of holding temperature, the prepared porous carbons had larger specific surface area and became more effective. Kinetic analysis revealed that adsorption kinetics obeyed the pseudo-second order kinetic model and adsorption equilibrium could reach within 1 h. The studies on isotherm indicated that the adsorption process could be best described by the Langmuir isotherm model and the maximum adsorption capacities was 598.8 mg g-1. Thermodynamic parameters demonstrated that the adsorption process was exothermic and spontaneous. Moreover, the porous carbon could effectively remove some other common dyes. Importantly, the prepared porous carbon was able to remove 98% of chrysoidine from polluted river water and its adsorption efficiency was inappreciably influenced by the water matrix. These results shown that the hierarchically porous carbons synthesized from biomass in this study had a wide application in water treatment.

Influence of d-Amino Acids in Beer on Formation of Uric Acid.

Excessive intake of beer could increase serum uric acid levels, leading to high risk of gout, which was previously attributed to high purine content in beer. Recent reports that purine-rich vegetables and bean products do not cause higher uric acid levels do not support this theory. Why excessive intake of beer could increase a high risk of gout has been unclear. Other factors affecting the accumulation of uric acid in the blood have been explored. Beer contains relatively high levels of d-amino acids due to the racemization of l-amino acids induced by food processing. d-amino acid was catalyzed by d-amino acid oxidase to produce H2O2, which is further oxidized in the presence of Fe2+ to produce hydroxyl radicals, resulting in DNA damage and formation of a large amount of purine bases, which are oxidized to uric acid by a series of enzymes. Some food ingredients, such as vitamins and I-, prompt d-amino acids to form uric acid. d-amino acids in beer are one of the key factors responsible for the increase in uric acid levels. The biological response of d-amino acids could explain gout occurrence in beer drinkers.

Colorimetric and visual determination of Au(III) ions using PEGylated gold nanoparticles.

A highly selective method is described for the colorimetric determination of Au(III) ions in acidic solution using gold nanoparticles (AuNPs) functionalized with thiolated methoxy poly(ethylene glycol) (mPEG). The presence of Au(III) induces the aggregation of the PEG-AuNPs, and this is accompanied by a color change from wine red to blue, and a decrease in absorbance at 525 nm. This can be monitored spectrophotometrically and visually. Absorbance at 525 nm linearly drops in the 0.50 to 1.75 mg·L-1 Au(III) concentration range, with a 0.25 mg·L-1 detection limit. The method is surprisingly selective over other metal ions. It was successfully applied to the analysis of ore samples. Graphical Abstract ᅟ.

Mirror-Image Thymidine Discriminates against Incorporation of Deoxyribonucleotide Triphosphate into DNA and Repairs Itself by DNA Polymerases.

DNA polymerases are known to recognize preferably d-nucleotides over l-nucleotides during DNA synthesis. Here, we report that several general DNA polymerases catalyze polymerization reactions of nucleotides directed by the DNA template containing an l-thymidine (l-T). The results display that the 5'-3' primer extension of natural nucleotides get to the end at chiral modification site with Taq and Phanta Max DNA polymerases, but the primer extension proceeds to the end of the template catalyzed by Deep Vent (exo-), Vent (exo-), and Therminator DNA polymerases. Furthermore, templating l-nucleoside displays a lag in the deoxyribonucleotide triphosphate (dNTP) incorporation rates relative to natural template by kinetics analysis, and polymerase chain reactions were inhibited with the DNA template containing two or three consecutive l-Ts. Most interestingly, no single base mutation or mismatch mixture corresponding to the location of l-T in the template was found, which is physiologically significant because they provide a theoretical basis on the involvement of DNA polymerase in the effective repair of l-T that may lead to cytotoxicity.

Role of Secondary Particle Formation in the Persistence of Silver Nanoparticles in Humic Acid Containing Water under Light Irradiation.

The wide use of silver nanoparticles (AgNPs) leads to the increasing release of AgNPs into the environment. Dissolved organic matter (DOM) is a key factor affecting the behaviors and fate of AgNPs in the aquatic environment. However, the mechanisms for the DOM-mediated transformations of AgNPs are still not fully understood. In this study, we investigated the persistence of AgNPs in the aquatic environment in the presence of different concentrations of humic acid (HA) over periods of time up to 14 days. The Ag species were monitored and characterized by absorption spectrometry, transmission electron microscopy (TEM), inductively coupled plasma mass spectrometry (ICP-MS), and multicollector ICP-MS (MC-ICP-MS). Results showed that the long-term persistence of AgNPs in HA-containing water was determined by two critical concentrations of HA. When the HA concentration exceeded a lower critical value, AgNPs could be persistent in the solution, and a large number of AgNPs were formed secondarily from the HA-induced reduction of the Ag+ ions released from the primary AgNPs, causing a redistribution of the particle size. With the HA concentration above a higher critical value, AgNPs could persist in the solution without a significant change in particle size. Notably, we used Ag isotope fractionation to investigate the transformation mechanism of AgNPs. The natural isotopic analysis by MC-ICP-MS revealed that the size redistribution of AgNPs caused significant Ag isotope fractionation, which gave additional evidence for the proposed mechanisms. This study provides new insights into the environmental fate of engineered AgNPs and highlights the usefulness of stable isotope fractionation in environmental nanotechnology.

Dissipation behavior and risk assessment of butralin in soybean and soil under field conditions.

Dissipation behavior, final residue, and risk assessment of butralin in soybean, green soybean, plant, and soil were investigated. Butralin residues were extracted with acetonitrile and then soybean samples were detected with gas chromatography-mass spectrometer (GC-MS) and soil samples were determined with GC with nitrogen phosphorous detector (GC-NPD). The limit of quantification (LOQ) of the method was 0.01 mg/kg for soybean, green soybean, plant, and soil. Average recoveries ranged from 90.4 ~ 98.2% for green soybean, 86.2 ~ 86.6% for soybean, 86.0 ~ 98.8% for plant, and 85.0 ~ 106.8% for soil. The relative standard deviations (RSDs) were 2.0 ~ 7.2% for green soybean, 2.0 ~ 3.0% for soybean, 3.1 ~ 8.1% for plant, and 1.8 ~ 6.6% for soil. Half-lives of butralin in soil samples varied in the range of 11-22 days. At harvest time, final residues of butralin in soybean and green soybean were lower than LOQ. Risk assessment demonstrated that, at recommended dosage and frequency, butralin would not induce significant harm on humans. The study could be used as a quantitative basis for application of butralin on soybean.

Antibody-Free Colorimetric Detection of Total Aflatoxins in Rice Based on a Simple Two-Step Chromogenic Reaction.

The prevalently used immunoassays for fast screening of aftatoxins (AFs) usually cannot meet the requirement for simultaneous determination of total AFs (aflatoxin B1 + aflatoxin B2 + aflatoxin G1 + aflatoxin G2) due to the deficiency of highly group-specific antibodies. This paper describes a two-step chromogenic reaction based method to quantitatively detect total AFs in rice using colorimetric measurement without antibody. In the method, colorless AFs transform into green-colored indophenol products through the reaction with sodium hydroxide and 2,6-dibromoquinone-4-chloroimide (DBQC) successively, allowing selectively determining total AFs up to 3.9 µg/kg over other competitive mycotoxins under optimal conditions by a UV-vis spectrophotometer. In addition, the colorimetric measurement results of the rice samples agree well with that of a standard HPLC method, demonstrating the good reliability and applicability of the method. Uniquely, the method has potential for on-site detection of total AFs in rice when using a nylon membrane-based device.