How formaldehyde reacts with amino acids

Cysteine as an Innovative Biomarker for Kidney Injury

BACKGROUND

Kidney transplantation is a widely used treatment for end-stage kidney disease. Nevertheless, the incidence of acute kidney injury (AKI) in deceased donors poses a potential hazard because it significantly increases the risk of delayed graft function and potentially exerts an influence on the kidney allograft outcome. It is crucial to develop a diagnostic model capable of assessing the existence and severity of AKI in renal grafts. However, no suitable kidney injury markers have been developed thus far.

METHODS

We evaluated the efficacy of the molecular probe NPO-B, which selectively responds to cysteine, as a new diagnostic tool for kidney injury. We used an in vitro model using ischemia/reperfusion injury human kidney-2 cells and an in vivo ischemia/reperfusion injury mouse model. Additionally, cysteine was investigated using urine samples from deceased donors and living donors to assess the applicability of detection techniques to humans.

RESULTS

This study confirmed that the NPO-B probe effectively identified and visualized the severity of kidney injury by detecting cysteine in both in vitro and in vivo models. We observed that the fluorescence intensity of urine samples measured using NPO-B from the deceased donors who are at a high risk of renal injury was significantly stronger than that of the living donors.

CONCLUSIONS

If implemented in clinical practice, this new diagnostic tool using NPO-B can potentially enhance the success rate of kidney transplantation by accurately determining the extent of AKI in renal grafts.

Dual effects of endogenous formaldehyde on the organism and drugs for its removal

Endogenous formaldehyde (FA) is produced in the human body via various mechanisms to preserve healthy energy metabolism and safeguard the organism. However, endogenous FA can have several negative effects on the body through epigenetic alterations, including cancer growth promotion; neuronal, hippocampal and endothelial damages; atherosclerosis acceleration; haemopoietic stem cell destruction and haemopoietic cell production reduction. Certain medications with antioxidant effects, such as glutathione, vitamin E, resveratrol, alpha lipoic acid and polyphenols, lessen the detrimental effects of endogenous FA by reducing oxidative stress, directly scavenging endogenous FA or promoting its degradation. This study offers fresh perspectives for managing illnesses associated with endogenous FA exposure.

Nitrous oxide respiration in acidophilic methanotrophs

Aerobic methanotrophic bacteria are considered strict aerobes but are often highly abundant in hypoxic and even anoxic environments. Despite possessing denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we show that acidophilic methanotrophs can respire nitrous oxide (N2O) and grow anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. We study two strains that possess N2O reductase genes: Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6. We show that N2O respiration supports growth of Methylacidiphilum caldifontis at an extremely acidic pH of 2.0, exceeding the known physiological pH limits for microbial N2O consumption. Methylocella tundrae simultaneously consumes N2O and CH4 in suboxic conditions, indicating robustness of its N2O reductase activity in the presence of O2. Furthermore, in O2-limiting conditions, the amount of CH4 oxidized per O2 reduced increases when N2O is added, indicating that Methylocella tundrae can direct more O2 towards methane monooxygenase. Thus, our results demonstrate that some methanotrophs can respire N2O independently or simultaneously with O2, which may facilitate their growth and survival in dynamic environments. Such metabolic capability enables these bacteria to simultaneously reduce the release of the key greenhouse gases CO2, CH4, and N2O.

Cu-doped Fe3O4 nanoparticles for efficient detoxification of epsilon toxin: Toward substituting magnetically recyclable detoxifying agent for formaldehyde

This research presents the synthesis and characterization of Cu-doped Fe3O4 (Cu-Fe3O4) nanoparticles as a magnetically recoverable and reusable detoxifying agent for the efficient and long-lasting neutralization of bacterial toxins. The nanoparticles were synthesized using the combustion synthesis method and characterized through SEM, XRD, BET, TGA, and VSM techniques. The detoxification potential of Cu-Fe3O4 was compared with traditional formaldehyde (FA) in detoxifying epsilon toxin (ETx) from Clostridium perfringens Type D, the causative agent of enterotoxemia in ruminants. In vivo residual toxicity tests revealed that Cu-Fe3O4 could detoxify ETx at a concentration of 2.0 mg mL-1 within 4 days at room temperature (RT) and 2 days at 37 °C, outperforming FA (12 and 6 days at RT and 37 °C, respectively). Characterization studies using dynamic light scattering (DLS) and circular dichroism (CD) highlighted lower conformational changes in Cu-Fe3O4-detoxified ETx compared to FA-detoxified ETx. Moreover, Cu-Fe3O4-detoxified ETx exhibited exceptional storage stability at 4 °C and RT for 6 months, maintaining an irreversible structure with no residual toxicity. The particles demonstrated remarkable reusability, with the ability to undergo five continuous detoxification batches. This study provides valuable insights into the development of an efficient and safe detoxifying agent, enabling the production of toxoids with a native-like structure. The magnetically recoverable and reusable nature of Cu-Fe3O4 nanoparticles offers practical advantages for easy recovery and reuse in detoxification reactions.

Effect of formaldehyde exposure on phytochemical content and functional activity of Agaricus bisporus (Lge.) Sing

In this study, the effect of formaldehyde on phytochemical content and antioxidant activity of Agaricus bisporus was investigated. Synthetic compost based on wheat straw was prepared by fermentation and disinfection. After steam pasteurization, 5 g of A. bisporus mycelia were inoculated into 1 kg of compost. To determine the effects of formaldehyde, 2, 4, and 6% concentrations were added to the composts, while compost without formaldehyde was used for the control group. The harvesting period was set at 10 weeks. Total phenolic and flavonoid content, macro- and microelement profile, and phenolic content were analyzed in the harvested A. bisporus samples. Macro- and microelement content was determined by ICP-OES, and phenolic compound profile was determined by LC-MS/MS analysis. Formaldehyde levels in A. bisporus samples were determined by the acetylacetone spectrophotometry method. The antioxidant capacity of A. bisporus samples was determined by DPPH scavenging activity; antimutagenic effects of samples were determined by Allium test. Application of 2, 4, and 6% formaldehyde resulted in a 1.12-, 1.19-, and 2.07-fold reduction in total phenolic content, respectively. The total phenolic content was reduced between 34.4% and 71.8%. These changes were confirmed by LC-MS/MS analysis. Compounds such as protocatechuic acid, salicylic acid, ferulic acid, and 4-OH benzoic acid, which were detected in the control group, could not be detected in the samples treated with 6% formaldehyde, and it was found that the application of formaldehyde reduced the phenolic content. Similar changes were also observed in macro- and microelements, and significant changes in elemental contents were observed after formaldehyde application. While the presence of formaldehyde at a low level, which may be due to natural production, was detected in the control group, a residue of 11.41 ± 0.93 mg/kg was determined in the 6% FMD applied group. All these changes resulted in a decrease in the antioxidant activity of A. bisporus. The DPPH scavenging activity, which was determined in the range of 21.6-73.3% in the control samples, decreased to 12.3-56.7% in the samples treated with formaldehyde. These results indicate that the application of formaldehyde at different stages of A. bisporus cultivation leads to significant changes in the nutritional value and biological activity of A. bisporus.

Influence of Amino Acid Substitutions in Capsid Proteins of Coxsackievirus B5 on Free Chlorine and Thermal Inactivation

The sensitivity of enteroviruses to disinfectants varies among genetically similar variants and coincides with amino acid changes in capsid proteins, although the effect of individual substitutions remains unknown. Here, we employed reverse genetics to investigate how amino acid substitutions in coxsackievirus B5 (CVB5) capsid proteins affect the virus' sensitivity to free chlorine and heat treatment. Of ten amino acid changes observed in CVB5 variants with free chlorine resistance, none significantly reduced the chlorine sensitivity, indicating a minor role of the capsid composition in chlorine sensitivity of CVB5. Conversely, a subset of these amino acid changes located at the C-terminal region of viral protein 1 led to reduced heat sensitivity. Cryo-electron microscopy revealed that these changes affect the assembly of intermediate viral states (altered and empty particles), suggesting that the mechanism for reduced heat sensitivity could be related to improved molecular packing of CVB5, resulting in greater stability or altered dynamics of virus uncoating during infection.

Computational Design of an Electro-Organocatalyst for Conversion of CO2 into Formaldehyde

Density functional theory calculations employing a hybrid implicit/explicit solvation method were used to explore a new strategy for electrochemical conversion of CO2 using an electro-organocatalyst. A particular structural motif is identified that consists of an electron-rich vicinal enediamine (>N-C═C-N<) backbone, which is capable of activating CO2 by the formation of a C-C bond while subsequently facilitating the transfer of electrons from a chemically inert cathode to ultimately produce formaldehyde. Unlike transition metal-based electrocatalysts, the electro-organocatalyst is not constrained by scaling relations between the formation energies of activated CO2 and adsorbed CO, nor is it expected to be active for the competing hydrogen evolution reaction. The rate-limiting steps are found to occur during two proton-coupled electron transfer (PCET) sequences and are associated with the transfer of a proton from a proton transfer mediator to a carbon atom on the electro-organocatalyst. The difficulty of this step in the second PCET sequence necessitates an electrode potential of -0.85 V vs RHE to achieve the maximum turnover frequency. In addition, it is postulated that the electro-organocatalyst should also be capable of forming long-chain aldehydes by successively carrying out reductive aldol condensation to grow the alkyl chain one carbon at a time.

Aldehyde-mediated inhibition of asparagine biosynthesis has implications for diabetes and alcoholism

Patients with alcoholism and type 2 diabetes manifest altered metabolism, including elevated aldehyde levels and unusually low asparagine levels. We show that asparagine synthetase B (ASNS), the only human asparagine-forming enzyme, is inhibited by disease-relevant reactive aldehydes, including formaldehyde and acetaldehyde. Cellular studies show non-cytotoxic amounts of reactive aldehydes induce a decrease in asparagine levels. Biochemical analyses reveal inhibition results from reaction of the aldehydes with the catalytically important N-terminal cysteine of ASNS. The combined cellular and biochemical results suggest a possible mechanism underlying the low asparagine levels in alcoholism and diabetes. The results will stimulate research on the biological consequences of the reactions of aldehydes with nucleophilic residues.

Formaldehyde gas sensors based on a quartz crystal microbalance modified with aniline-doped polyvinyl acetate nanofibers

Real-time detection of formaldehyde in the atmosphere remains challenging. The available gaseous formaldehyde sensing methods offer limited sensitivity, selectivity, and robustness. We modified a quartz crystal microbalance (QCM) system for selective detection of formaldehyde in air. The QCM surface was functionalized with polyvinyl acetate (PVAc) nanofibers and doped with 2, 4, and 6 wt% aniline to improve the selectivity and sensitivity of the sensor. The chemical content and morphological structure of PVAc nanofibers doped with aniline were confirmed by Fourier-transform infrared (FTIR) spectroscopy, energy-dispersive X-ray (EDX) spectroscopy, and scanning electron microscopy (SEM). The results showed that the modified QCM sensor had a sensitivity of 0.056 Hz ppm-1 with a response and recovery times of 200 s and 90 s, respectively. It gave limits of detection (LOD) and limit of quantification (LOQ) of 28 ppm and 96 ppm, respectively. Moreover, the modified QCM was selective towards formaldehyde compared to the other gases. The current workplace exposure limit (WEL) for formaldehyde is 2 ppm, with a time-weighted average over eight hours. Future work will focus on improving the reported QCM sensor to meet the required LOD for formaldehyde detection in the environment and industrial sites.

Activatable Near-Infrared Versatile Fluorescent and Chemiluminescent Dyes Based on the Dicyanomethylene-4H-pyran Scaffold: From Design to Imaging and Theranostics

Activatable fluorescent and chemiluminescent dyes with near-infrared emission have indispensable roles in the fields of bioimaging, molecular prodrugs, and phototheranostic agents. As one of the most popular fluorophore scaffolds, the dicyanomethylene-4H-pyran scaffold has been applied to fabricate a large number of versatile activatable optical dyes for analytes detection and diseases diagnosis and treatment by virtue of its high photostability, large Stokes shift, considerable two-photon absorption cross-section, and structural modifiability. This review discusses the molecular design strategies, recognition mechanisms, and both in vitro and in vivo bio-applications (especially for diagnosis and therapy of tumors) of activatable dicyanomethylene-4H-pyran dyes. The final section describes the current shortcomings and future development prospects of this topic.

Isolation and detection of DNA-protein crosslinks in mammalian cells

DNA-protein crosslinks (DPCs) are toxic DNA lesions wherein a protein is covalently attached to DNA. If not rapidly repaired, DPCs create obstacles that disturb DNA replication, transcription and DNA damage repair, ultimately leading to genome instability. The persistence of DPCs is associated with premature ageing, cancer and neurodegeneration. In mammalian cells, the repair of DPCs mainly relies on the proteolytic activities of SPRTN and the 26S proteasome, complemented by other enzymes including TDP1/2 and the MRN complex, and many of the activities involved are essential, restricting genetic approaches. For many years, the study of DPC repair in mammalian cells was hindered by the lack of standardised assays, most notably assays that reliably quantified the proteins or proteolytic fragments covalently bound to DNA. Recent interest in the field has spurred the development of several biochemical methods for DPC analysis. Here, we critically analyse the latest techniques for DPC isolation and the benefits and drawbacks of each. We aim to assist researchers in selecting the most suitable isolation method for their experimental requirements and questions, and to facilitate the comparison of results across different laboratories using different approaches.

Exquisite exposure: Formaldehyde as a metabolic regulator

Throughout life, whether through external consumption or internal production, we are exposed to different reactive metabolites considered toxic to the body. Pham et al.1 uncover metabolic regulation by one such harmful metabolite: formaldehyde.

One enzyme, many faces: urease is also canatoxin

Ureases catalyze the hydrolysis of urea into carbamate and ammonia. Well-conserved proteins, most plant ureases are hexamers of a single chain subunit, like the most abundant isoform of the jack bean (Canavalia ensiformis) urease (JBU). Canatoxin (CNTX) was originally isolated from these seeds as a neurotoxic protein, and later characterized as an isoform of JBU with lower molecular mass and enzyme activity. Inactive CNTX oligomers form upon storage and stabilization of CNTX was achieved by treatment with low concentration of formaldehyde, avoiding its oligomerization. Here, nano-LC-MS/MS-based peptide analysis of CNTX revealed 804 amino acids identical to those of JBU's sequence (840 amino acids). De novo sequencing of CNTX revealed 15 different peptides containing substitution of amino acid residues, denoting CNTX as a product of a paralog gene of JBU. The MS/MS analysis of formaldehyde-treated CNTX showed that amino acid residues located at the trimer-trimer interface of JBU's hexamer were modified. The data confirmed that CNTX is an isoform of JBU and elucidated that stabilization by formaldehyde treatment occurs by modification of amino acids at the protein's surface that prevents the formation of the hexamer and of higher molecular mass inactive aggregates. HIGHLIGHTSCanatoxin (CNTX) is an isoform of jack bean urease (JBU, hexamer of 90 kDa chains)MS/MS sequencing of CNTX showed 804 amino acids identical in JBU (840 residues)Formaldehyde treatment of CNTX stabilizes its toxicity and avoids oligomerizationModified amino acid residues in CNTX are at the trimer-trimer interface of JBUCommunicated by Ramaswamy H. Sarma.

N-Acyloxymethyl-phthalimides deliver genotoxic formaldehyde to human cells

Formaldehyde is a pollutant and human metabolite that is toxic at high concentrations. Biological studies on formaldehyde are hindered by its high reactivity and volatility, which make it challenging to deliver quantitatively to cells. Here, we describe the development and validation of a set of N-acyloxymethyl-phthalimides as cell-relevant formaldehyde delivery agents. These esterase-sensitive compounds were similarly or less inhibitory to human cancer cell growth than free formaldehyde but the lead compound increased intracellular formaldehyde concentrations, increased cellular levels of thymidine derivatives (implying increased formaldehyde-mediated carbon metabolism), induced formation of cellular DNA-protein cross-links and induced cell death in pancreatic cancer cells. Overall, our N-acyloxymethyl-phthalimides and control compounds provide an accessible and broadly applicable chemical toolkit for formaldehyde biological research and have potential as cancer therapeutics.

Formaldehyde regulates S-adenosylmethionine biosynthesis and one-carbon metabolism

One-carbon metabolism is an essential branch of cellular metabolism that intersects with epigenetic regulation. In this work, we show how formaldehyde (FA), a one-carbon unit derived from both endogenous sources and environmental exposure, regulates one-carbon metabolism by inhibiting the biosynthesis of S-adenosylmethionine (SAM), the major methyl donor in cells. FA reacts with privileged, hyperreactive cysteine sites in the proteome, including Cys120 in S-adenosylmethionine synthase isoform type-1 (MAT1A). FA exposure inhibited MAT1A activity and decreased SAM production with MAT-isoform specificity. A genetic mouse model of chronic FA overload showed a decrease n SAM and in methylation on selected histones and genes. Epigenetic and transcriptional regulation of Mat1a and related genes function as compensatory mechanisms for FA-dependent SAM depletion, revealing a biochemical feedback cycle between FA and SAM one-carbon units.

Perspectives for the creation of a new type of vaccine preparations based on pseudovirus particles using polio vaccine as an example

Traditional antiviral vaccines are currently created by inactivating the virus chemically, most often using formaldehyde or β-propiolactone. These approaches are not optimal since they negatively affect the safety of the antigenic determinants of the inactivated particles and require additional purification stages. The most promising platforms for creating vaccines are based on pseudoviruses, i.e., viruses that have completely preserved the outer shell (capsid), while losing the ability to reproduce owing to the destruction of the genome. The irradiation of viruses with electron beam is the optimal way to create pseudoviral particles. In this review, with the example of the poliovirus, the main algorithms that can be applied to characterize pseudoviral particles functionally and structurally in the process of creating a vaccine preparation are presented. These algorithms are, namely, the analysis of the degree of genome destruction and coimmunogenicity. The structure of the poliovirus and methods of its inactivation are considered. Methods for assessing residual infectivity and immunogenicity are proposed for the functional characterization of pseudoviruses. Genome integrity analysis approaches, atomic force and electron microscopy, surface plasmon resonance, and bioelectrochemical methods are crucial to structural characterization of the pseudovirus particles.

A facile bioorthogonal chemistry-based reversible to irreversible strategy to surmount the dilemma between injectability and stability of hyaluronic acid hydrogels

Injectable and stable hydrogels have great promise for clinical applications. Fine-tuning the injectability and the stability of the hydrogels at different stages has been challenging due to the limited number of coupling reactions. A distinct "reversible to irreversible" concept using a thiazolidine-based bioorthogonal reaction between 1,2-aminothiols and aldehydes in physiological conditions to surmount the dilemma between injectability and stability is presented for the first time. Upon mixing aqueous solutions of aldehyde-functionalized hyaluronic acid (SA-HA) and cysteine-capped ethylenediamine (DI-Cys), SA-HA/DI-Cys hydrogels formed through reversible hemithioacetal crosslinking within 2 min. The reversible kinetic intermediate facilitated thiol-triggered gel-to-sol transition, shear-thinning and injectability of the SA-HA/DI-Cys hydrogel but then converted to the irreversible thermodynamic network after injection, thereby permitting the resulting gel with improved stability. As compared to the Schiff base hydrogels, the hydrogels generated from this simple, yet effective concept awarded improved protection to the embedded mesenchymal stem cells and fibroblast during injection, retained the cells homogeneously within the gel, and allowed them further proliferation in vitro and in vivo. There is potential for the proposed approach of "reversible to irreversible" based on thiazolidine chemistry to be applied as a general coupling technique for developing injectable and stable hydrogels for biomedical applications.

Quantitative detection of formaldehyde using solid phase microextraction gas chromatography-mass spectrometry coupled to cysteamine scavenging

Formaldehyde (HCHO) is a toxic and carcinogenic pollutant and human metabolite that reacts with biomolecules under physiological conditions. Quantifying HCHO is essential for ongoing biological and biomedical research on HCHO; however, its reactivity, small size and volatility make this challenging. Here, we report a novel HCHO detection/quantification method that couples cysteamine-mediated HCHO scavenging with SPME GC-MS analysis. Our NMR studies confirm cysteamine as an efficient and selective HCHO scavenger that out-competes O-(2,3,4,5,6-pentafluorobenzyl)hydroxylamine, the most commonly used scavenger, and forms a stable thiazolidine amenable to GC-MS quantification. Validation of our GC-MS method using FDA and EMA guidelines revealed detection and quantification limits in the nanomolar and micromolar ranges respectively, while analysis of bacterial cell lysate confirmed its applicability in biological samples. Overall, our studies confirm that cysteamine scavenging coupled to SPME GC-MS analysis provides a sensitive and chemically robust method to quantify HCHO in biological samples.

High Efficiency of Formaldehyde Removal and Anti-bacterial Capability Realized by a Multi-Scale Micro-Nano Channel Structure in Hybrid Hydrogel Coating Cross-Linked on Microfiber-Based Polyurethane

Inspired by the transpiration in the tree stem having a vertical and porous channel structure, high efficiency of formaldehyde removal is realized by the multi-scale micro-nano channel structure in a hybrid P(AAm/DA)-Ag/MgO hydrogel coating cross-linked on microfiber-based polyurethane. The present multi-scale channel structure is formed by a joint effect of directional freezing and redox polymerization as well as nanoparticles-induced porosity. Due to the large number of vertically aligned channels of micrometer size and an embedded porous structure of nanometer size, the specific surface area is significantly increased. Therefore, formaldehyde from solution can be rapidly adsorbed by the amine group in the hydrogels and efficiently degraded by the Ag/MgO nanoparticles. By only immersing in formaldehyde solution (0.2 mg mL^-1) for 12 h, 83.8% formaldehyde is removed by the hybrid hydrogels with a multi-scale channel structure, which is 60.8% faster than that observed in hydrogels without any channel structure. After cross-linking the hybrid hydrogels with a multi-scale channel structure to microfiber-based polyurethane and exposing to the formaldehyde vapor atmosphere, 79.2% formaldehyde is removed in 12 h, which is again 11.2% higher than that observed in hydrogels without any channel structure. Unlike the traditional approaches to remove formaldehyde by the light catalyst, no external conditions are required in our present hybrid hydrogel coating, which is very suitable for indoor use. In addition, due to the formation of free radicals by the Ag/MgO nanoparticles, the cross-linked hybrid hydrogel coating on polyurethane synthetic leather also shows good anti-bacterial capability. 99.99% of Staphylococcus aureus can be killed on the surface. Based on the good ability to remove formaldehyde and to kill bacteria, the obtained microfiber-based polyurethane cross-linked with a hybrid hydrogel coating containing a multi-scale channel structure can be used in a broad field of applications, such as furniture and car interior parts, to simultaneously solve the indoor air pollution and hygiene problems.

Disease-Specific α-Synuclein Seeding in Lewy Body Disease and Multiple System Atrophy Are Preserved in Formaldehyde-Fixed Paraffin-Embedded Human Brain

Recent studies have been able to detect α-synuclein (αSyn) seeding in formaldehyde-fixed paraffin-embedded (FFPE) tissues from patients with synucleinopathies using seed amplification assays (SAAs), but with relatively low sensitivity due to limited protein extraction efficiency. With the aim of introducing an alternative option to frozen tissues, we developed a streamlined protein extraction protocol for evaluating disease-specific seeding in FFPE human brain. We evaluated the protein extraction efficiency of different tissue preparations, deparaffinizations, and protein extraction buffers using formaldehyde-fixed and FFPE tissue of a single Lewy body disease (LBD) subject. Alternatively, we incorporated heat-induced antigen retrieval and dissociation using a commercially available kit. Our novel protein extraction protocol has been optimized to work with 10 sections of 4.5-µm-thickness or 2-mm-diameter micro-punch of FFPE tissue that can be used to seed SAAs. We demonstrated that extracted proteins from FFPE still preserve seeding potential and further show disease-specific seeding in LBD and multiple system atrophy. To the best of our knowledge, our study is the first to recapitulate disease-specific αSyn seeding behaviour in FFPE human brain. Our findings open new perspectives in re-evaluating archived human brain tissue, extending the disease-specific seeding assays to larger cohorts to facilitate molecular subtyping of synucleinopathies.

N-acetylcysteine modulates redox imbalance and inflammation in macrophages and mice exposed to formaldehyde

This study aimed to evaluate the protective role of N-acetylcysteine (NAC) in cells and mice exposed to formaldehyde. For the in vitro study, J774A.1 macrophages cells were incubated for 8, 16 and 24 h with formaldehyde or NAC to assess cell viability and reactive oxygen species (ROS). In the in vivo study, C57BL/6 mice (n = 48) were divided into 6 groups: control (CG), vehicle (VG) that received saline by orogastric gavage, a group exposed to formaldehyde 1% (FG) and formaldehyde exposed groups that received NAC at doses of 100, 150 and 200 mg/Kg (FN100, FN150 and FN200) for a period of 5 days. In vitro, formaldehyde promoted a decrease in cell viability and increased ROS, while NAC reduced formaldehyde-induced ROS production. Animals exposed to formaldehyde presented higher leukocyte counts in the blood and in the bronchoalveolar lavage fluid, and promoted secretion of inflammatory markers IL-6, IL-15, and IL-10. The exposure to formaldehyde also promoted redox imbalance and oxidative damage characterized by increased activities of superoxide dismutase, catalase, decreased GSH/GSSG ratio, as well as it increased levels of protein carbonyls and lipid peroxidation. NAC administration after formaldehyde exposure attenuated oxidative stress markers, secretion of inflammatory mediators and lung inflammation. In conclusion, both in in vitro and in vivo models, NAC administration exerted protective effects, which modulated the inflammatory response and redox imbalance, thus preventing the development airway injury induced by formaldehyde exposure.

Impact of formaldehyde, acetaldehyde, and N-(3-(Dimethylamino)propyl)methacrylamide on the efficacy of the human derived coagulation factor IX

Polymer-borne leachables such as formaldehyde, acetaldehyde, and N-3-(Dimethylamino)propyl)methacrylamide (DMAPMA) may interact with therapeutic proteins. In this study, the leachables were spiked into human derived coagulation factor IX (FIX) at concentrations of 1, 10, 50, 100, and 500 µg/mL, corresponding to a leachable - FIX ratio of 0.5, 5, 25, 50 and 250 %, respectively. The spiked samples were visually inspected, and pH was measured. No visual effects were observed, and pH was within the drug product's specified range. Recovery experiments were performed and no loss of leachables was identified. Protein structure analysis revealed that formaldehyde reacted with lysine contained in two different positions of FIX, in a concentration-dependent manner starting at 10 µg/mL (5 %). The clotting activity of FIX was measured. The activity of the samples spiked with 500 µg/mL (250 %) of formaldehyde dropped by more than half. The activity of the samples spiked with acetaldehyde began to drop at 50 µg/mL (25 %) and continued to decline in concentration-dependent manner. DMAPMA did not impair the activity of FIX. The findings conclude that depending on the concentration, some leachables may react with or modify therapeutic proteins, potentially causing an undesired pharmacological effect however, this is specific to each protein.

Formaldehyde reacts with N-terminal proline residues to give bicyclic aminals

Formaldehyde (HCHO) is a potent electrophile that is toxic above threshold levels, but which is also produced in the nuclei of eukaryotic cells by demethylases. We report studies with the four canonical human histones revealing that histone H2B reacts with HCHO, including as generated by a histone demethylase, to give a stable product. NMR studies show that HCHO reacts with the N-terminal proline and associated amide of H2B to give a 5,5-bicyclic aminal that is relatively stable to competition with HCHO scavengers. While the roles of histone modification by this reaction require further investigation, we demonstrated the potential of N-terminal aminal formation to modulate protein function by conducting biochemical and cellular studies on the effects of HCHO on catalysis by 4-oxalocrotonate tautomerase, which employs a nucleophilic N-terminal proline. The results suggest that reactions of N-terminal residues with HCHO and other aldehydes have potential to alter protein function.

A Novel Strategy Based on Permanent Protein Modifications Induced by Formaldehyde for Food Safety Analysis

The illegal additions of chemicals in food products are serious incidents threatening current public safety. To date, ideal methods to determine permanent traces of prohibited chemicals in foods are still lacking. For example, formaldehyde (FA) can be added illegally as a food preservative. However, most current methods that are dependent on the direct detection of FA are not able to determine if FA has ever been added once food products are rinsed completely. Herein, we present a novel approach relying upon protein modifications induced by FA (PMIF) to examine FA in foods. We reveal the entire catalog of PMIFs in food products by combining mass spectrometry analysis with unrestrictive identification of protein modifications. Consequently, four obvious PMIFs were identified and confirmed as markers to discriminate the addition of FA in foods. Our study demonstrates that the approach based on PMIFs enables detecting the imprinted trace of FA even if the food products have been washed thoroughly. Our work presents a novel strategy for analysis of chemical additives, offering broad potential applications in protein analysis and food safety.

Cytotoxicity of a Novel Compound Produced in Foods via the Reaction of Amino Acids with Acrolein along with Formaldehyde

Acrolein (ACR) and formaldehyde (FA) are toxic aldehydes co-produced in foods. This work found that amino acids, the nucleophiles ubiquitously existing in foods, can react simultaneously with them. Six amino acids, including γ-aminobutyric acid (GABA), glycine, alanine, serine, threonine, and glutamine, can scavenge ACR and FA at 37, 85, and 160 °C. GABA had the highest scavenging capacity for ACR and FA, by 79 and 13% at 37 °C for 2 h, and 99 and 48% at 160 °C for 30 min, respectively. Moreover, a new type of compound with a basic structure of 5-formyl-3-methylene-3,6-dihydropyridin was identified in all reactions and formed by 1 molecule of FA and amino acid and 2 molecules of ACR. The content of this compound was higher than that of free ACR in typical thermally processed foods. Moreover, the compounds produced from different amino acids showed different cytotoxicity values. In gastric epithelial and human intestinal epithelial cell lines, the cytotoxicity values of serine-sourced and threonine-sourced products were lower than that of ACR but higher than that of FA, whereas others had less toxicity compared with the two aldehydes. Considering that the content of serine-sourced products was the highest in almost all tested foods, their safety needs to be evaluated.

Do more with Less: Improving High Parameter Cytometry Through Overnight Staining

Recent advances in flow cytometry have allowed high-dimensional characterization of biological phenomena, enabling breakthroughs in a multitude of fields. Despite the appreciation of the unique properties of antigens and fluorophores in high-parameter panel design, staining conditions are often standardized for short surface stains, regardless of antibody affinity or antigen accessibility. Here, we demonstrate how increasing antibody incubation times can lead to substantial improvements in sensitivity, maintaining specificity, and reducing background, while also significantly reducing the costs of high-parameter cytometry panels. Furthermore, overnight staining reduces the influence of interexperimental variability, assisting accurate pooling over experiments over extended time courses. We provide guidance on how to optimize staining conditions for diverse antigens, including how different fixation strategies can affect epitope accessibility. Overnight staining can thus substantially improve the resolution, repeatability, and cost-effectiveness of high-parameter cytometry. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.

A biophysical basis for the emergence of the genetic code in protocells

The origin of the genetic code is an abiding mystery in biology. Hints of a 'code within the codons' suggest biophysical interactions, but these patterns have resisted interpretation. Here, we present a new framework, grounded in the autotrophic growth of protocells from CO₂ and H₂. Recent work suggests that the universal core of metabolism recapitulates a thermodynamically favoured protometabolism right up to nucleotide synthesis. Considering the genetic code in relation to an extended protometabolism allows us to predict most codon assignments. We show that the first letter of the codon corresponds to the distance from CO₂ fixation, with amino acids encoded by the purines (G followed by A) being closest to CO₂ fixation. These associations suggest a purine-rich early metabolism with a restricted pool of amino acids. The second position of the anticodon corresponds to the hydrophobicity of the amino acid encoded. We combine multiple measures of hydrophobicity to show that this correlation holds strongly for early amino acids but is weaker for later species. Finally, we demonstrate that redundancy at the third position is not randomly distributed around the code: non-redundant amino acids can be assigned based on size, specifically length. We attribute this to additional stereochemical interactions at the anticodon. These rules imply an iterative expansion of the genetic code over time with codon assignments depending on both distance from CO₂ and biophysical interactions between nucleotide sequences and amino acids. In this way the earliest RNA polymers could produce non-random peptide sequences with selectable functions in autotrophic protocells.

A novel approach for the bioanalysis of short-lived aldehydes

Background: The instability of aldehydes in biological matrices is associated with their reactions with thiol and amino moieties in proteins. This chemical reaction is reversible by nature and highly pH dependent. Method: A novel approach that includes protein precipitation with an acidic solution of acetonitrile/water/formic acid (85/14/1; v/v/v) was developed to efficiently recover Aldehyde-1 from plasma by shifting the equilibrium toward the formation of the free form. Results: This enabled the support of two GLP studies where Aldehyde-1 was administered to mice. The recovery of Aldehyde-1 from plasma exceeded 88% at three concentration levels. Plasma stability was confirmed at ambient conditions for 24 h and in the freezer for at least 43 (-20°C) and 64 (-70°C) days.

A Rapid Fluorescence Sensor for the Direct Quantification of Rongalite in Foodstuffs

Rongalite was reported illegally used as a food additive for bleaching purposes and improving the tenderness of foodstuffs, which may endanger public health. At present, rongalite was mostly detected by indirect methods via derivatization or determining its decomposition products. In this study, we developed a new fluorescence sensor for the direct quantification of rongalite based on the principles: (1) dopamine reacts with resorcinol and generates strong fluorophore (azamonardine); (2) rongalite could inhibit the production of fluorophores and then result in lower fluorescence intensity. Hence, the rongalite concentration was inversely proportional to fluorescence intensity of fluorophore. Several crucial reaction conditions of fluorescence sensor were further optimized, such as dopamine and resorcinol concentration, pH values, and reaction time. Under the optimal conditions, the limit of detection of fluorescence sensor was 0.28–0.38 μg/g in vermicelli, wheat and rice powder samples, exhibiting almost 3.5-fold improvement compared to that of lateral flow immunoassay. Moreover, the detection time was substantially decreased to 20 min. The recoveries in spiked samples were 80.7–102.1% with a coefficient of variation of less than 12.6%. In summary, we developed a direct, high throughput, selective and accurate fluorescence sensor that poses a promising application for the rapid detection of rongalite in foodstuffs.

A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative

Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on amino acid residue modifications in CHT also indicate towards the formation of multiple ANS binding site. The docking model also predicted no change in binding behavior for the substrate Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) at the active site upon formalin induced amino acid cross-linking.

The SOS response-associated peptidase (SRAP) domain of YedK catalyzes ring opening of abasic sites and reversal of its DNA-protein crosslink

Apurinic/apyrimidinic (AP, or abasic) sites in DNA are one of the most common forms of DNA damage. AP sites are reactive and form cross-links to both proteins and DNA, are prone to strand breakage, and inhibit DNA replication and transcription. The replication-associated AP site repair protein HMCES protects cells from strand breaks, inhibits mutagenic translesion synthesis, and participates in repair of interstrand DNA cross-links derived from AP sites by forming a stable thiazolidine DNA–protein cross-link (DPC) to AP sites in single-stranded DNA (ssDNA). Despite the importance of HMCES to genome maintenance and the evolutionary conservation of its catalytic SRAP (SOS Response Associated Peptidase) domain, the enzymatic mechanisms of DPC formation and resolution are unknown. Using the bacterial homolog YedK, we show that the SRAP domain catalyzes conversion of the AP site to its reactive, ring-opened aldehyde form, and we provide structural evidence for the Schiff base intermediate that forms prior to the more stable thiazolidine. We also report two new activities, whereby SRAP reacts with polyunsaturated aldehydes at DNA 3′-ends generated by bifunctional DNA glycosylases and catalyzes direct reversal of the DPC to regenerate the AP site, the latter of which we observe in both YedK and HMCES-SRAP proteins. Taken together, this work provides insights into possible mechanisms by which HMCES DPCs are resolved in cells.

Protective role of electrophile-reactive glutathione for DNA damage repair inhibitory effect of dibromoacetonitrile

Dibromoacetonitrile (DBAN) is a disinfection byproduct (DBP) and linked with cancer in rodents, but the mechanism of its carcinogenicity has not been fully elucidated. We recently reported that DBAN induced inhibition of nucleotide excision repair (NER). In this study, we investigated if glutathione (GSH) is involved in the DBAN-induced inhibition of NER. Human keratinocytes HaCaT were pretreated with L-buthionine-(S,R)-sulfoximine (BSO) to deplete intracellular GSH. BSO treatment markedly potentiated the DBAN-induced NER inhibition as well as intracellular oxidation. The recruitment of NER proteins (transcription factor IIH, and xeroderma pigmentosum complementation group G) to DNA damage sites was inhibited by DBAN, which was further exacerbated by BSO treatment. Our results suggest that intracellular GSH protects cells from DBAN-induced genotoxicity including inhibition of DNA damage repair.

Approaches to Formaldehyde Measurement: From Liquid Biological Samples to Cells and Organisms

Formaldehyde (FA) is the simplest aldehyde present both in the environment and in living organisms. FA is an extremely reactive compound capable of protein crosslinking and DNA damage. For a long time, FA was considered a “biochemical waste” and a by-product of normal cellular metabolism, but in recent decades the picture has changed. As a result, the need arose for novel instruments and approaches to monitor and measure not only environmental FA in water, cosmetics, and household products, but also in food, beverages and biological samples including cells and even organisms. Despite numerous protocols being developed for in vitro and in cellulo FA assessment, many of them have remained at the “proof-of-concept” stage. We analyze the suitability of different methods developed for non-biological objects, and present an overview of the recently developed approaches, including chemically-synthesized probes and genetically encoded FA-sensors for in cellulo and in vivo FA monitoring. We also discuss the prospects of classical methods such as chromatography and spectrophotometry, and how they have been adapted in response to the demand for precise, selective and highly sensitive evaluation of FA concentration fluctuations in biological samples. The main objectives of this review is to summarize data on the main approaches for FA content measurement in liquid biological samples, pointing out the advantages and disadvantages of each method; to report the progress in development of novel molecules suitable for application in living systems; and, finally, to discuss genetically encoded FA-sensors based on existing natural biological FA-responsive elements.

Construction of Complex Macromulticyclic Peptides via Stitching with Formaldehyde and Guanidine

There is a growing interest in constructing multicyclic peptide structures to expand the chemical space of peptides. Conventional strategies for constructing large peptide structures are limited by the typical reliance on the inflexible coupling between premade templates equipped with fixed reactive handles and peptide substrates via cysteine anchors. Herein, we report the development of a facile three-component condensation reaction of primary alkyl amine, formaldehyde, and guanidine for construction of complex macromulticyclic peptides with novel topologies via lysine anchors. Moreover, the reaction sequences can be orchestrated in different anchor combinations and spatial arrangements to generate various macrocyclic structures crosslinked by distinct fused tetrahydrotriazine linkages. The macrocyclization reactions are selective, efficient, versatile, and workable in both organic and aqueous media. Thus, the condensation reaction provides a smart tool for stitching native peptides in situ using simple methylene threads and guanidine joints in a flexible and programmable manner.

Connecting algal polysaccharide degradation to formaldehyde detoxification

Formaldehyde is a toxic metabolite that is formed in large quantities during bacterial utilization of the methoxy sugar 6‐O‐methyl‐d‐galactose, an abundant monosaccharide in the red algal polysaccharide porphyran. Marine bacteria capable of metabolizing porphyran must therefore possess suitable detoxification systems for formaldehyde. We demonstrate here that detoxification of formaldehyde in the marine Flavobacterium Zobellia galactanivorans proceeds via the ribulose monophosphate pathway. Simultaneously, we show that the genes encoding the key enzymes of this pathway are important for maintaining high formaldehyde resistance. Additionally, these genes are upregulated in the presence of porphyran, allowing us to connect porphyran degradation to the detoxification of formed formaldehyde.

Aquaporin-Inspired CPs/AAO Nanochannels for the Effective Detection of HCHO: Importance of a Hydrophilic/Hydrophobic Janus Device for High-Performance Sensing

Probe reactivity has long been considered to play a key role in artificial nanochannel sensors, but systematic studies of membrane wettability on detection performance are currently lacking. Inspired by biological aquaporins, we developed an effective strategy to regulate the hydrophilic/hydrophobic balance by the controllable in situ assembly of coordination polymers (CPs) using BDC-NH₂ on anodic aluminum oxide (AAO) nanochannels to promote HCHO detection. We found that the hydrophobic/hydrophilic balance in CP/AAO heterosomes plays significant roles in the effective detection of HCHO. The hydrophobic AAO barrier layer is necessary to support the confinement effect, while the hydrophilic CP surface is favorable for HCHO to access the channels and then condense with the responsive amine to generate a new imine. The optimized CP/AAO Janus device shows excellent performance in the quantitative analysis of HCHO over a wide range from 100 pM to 1 mM by monitoring the rectified ionic current.

Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens

Objectives

Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins.

Methods

Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS).

Results

Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval.

Conclusions

Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12014-022-09346-0.

Chiral Water-Soluble Molecular Capsules With Amphiphilic Interiors

We present the synthesis of new chiral water-soluble dimeric capsules by the multicomponent Mannich reaction between charged amino acids (glutamic acid or arginine), resorcinarene, and formaldehyde and by subsequent self-assembly. The zwitterionic character of the backbones enables electrostatic interactions between arms and induces self-assembly of dimeric capsules, namely, (L-ArgR)₂ and (L-GluR)₂, in water with a wide range of pH, as demonstrated by NMR, diffusion coefficient measurement, and circular dichroism. The assembly/disassembly processes are fast on the NMR timescale. This mode of dimerization leaves side chains available for additional interactions and creates chiral cavities of mixed hydrophobic/hydrophilic character. According to this characteristic, capsules do not bind fully nonpolar or fully polar guests but effectively encapsulate a variety of chiral molecules with mixed polar/apolar characters (aliphatic and aromatic aldehydes, epoxides, alcohols, carboxylic acids, amines, and amino acids) with moderate strength. We also demonstrate the formation of heterocapsules (GluR) (ArgR) (homo- and heterochiral) that utilize additional interactions between charged acidic and basic side chains and have better encapsulation properties than those of the homodimers.

Development of a bifunctional edible coating for formaldehyde scavenging and preservation of aquatic products

BACKGROUND

Although exogenous and endogenous formaldehyde in squid has led to severe health threat, an in-depth study on natural edible scavengers for formaldehyde in squid is still lacking.

RESULTS

Response surface methodology (RSM) combined with experimental verification approaches was applied to obtain an optimal 'recipe' to achieve formaldehyde removal rate of >85%: 6 mg mL^-1 tea polyphenols, 20 mg mL^-1 chitosan, 3:2 (v/v) tea polyphenols and chitosan, a pH value of 3 and 60 min treatment time. Apart from the capability of removing formaldehyde, the scavenger derived from natural food exhibited a significant preservation effect (extension of preservation time up to 40%) on squid during chilled storage, and was safe and environmentally friendly. Meanwhile, a synergetic effect of the two components on scavenging formaldehyde was unraveled by multimolecular infrared spectroscopy.

CONCLUSION

An edible and bifunctional reagent composed of tea polyphenols and chitosan was developed for simultaneously removing artificially added or endogenous formaldehyde and for preservation of squid. The bifunctional coating shows promise as a formaldehyde scavenger and green preservative for aquatic products. © 2021 Society of Chemical Industry.

Structure–Activity Relationship of Cytotoxic Natural Products from Indonesian Marine Sponges

Indonesian marine natural products have been one of the most promising sources in the race to obtain potential drugs for cancer treatment. One of the primary producers of cytotoxic compounds is sponges. However, there are still limited sources of comprehensive reviews related to the relationship between the structure of isolated compounds and their cytotoxic activity. This review remarks the attempt to provide a preliminary guidance from the perspective of structure–activity relationship and its participation on marine natural products research. This guidance is segregated by the compound’s classes and their cytotoxic targets to obtain and organized a reliable summary of inter-study of the isolated compounds and their cytotoxicity. Structure–activity relationship is well-known for its ability to tune the bioactivity of a specific compound, especially on synthetic organic chemistry and in silico study but rarely used on natural product chemistry. The present review is intended to narrow down the endless possibilities of cytotoxicity by giving a predictable structure–activity relationship for active compounds. In addition, bioactive framework leads were selected by uncovering a noticeable structure–activity relationship with the intervention of cytotoxic agents from natural sources, especially Indonesian marine sponge.

Unravelling Formaldehyde Metabolism in Bacteria: Road towards Synthetic Methylotrophy

Formaldehyde metabolism is prevalent in all organisms, where the accumulation of formaldehyde can be prevented through the activity of dissimilation pathways. Furthermore, formaldehyde assimilatory pathways play a fundamental role in many methylotrophs, which are microorganisms able to build biomass and obtain energy from single- and multicarbon compounds with no carbon–carbon bonds. Here, we describe how formaldehyde is formed in the environment, the mechanisms of its toxicity to the cells, and the cell’s strategies to circumvent it. While their importance is unquestionable for cell survival in formaldehyde rich environments, we present examples of how the modification of native formaldehyde dissimilation pathways in nonmethylotrophic bacteria can be applied to redirect carbon flux toward heterologous, synthetic formaldehyde assimilation pathways introduced into their metabolism. Attempts to engineer methylotrophy into nonmethylotrophic hosts have gained interest in the past decade, with only limited successes leading to the creation of autonomous synthetic methylotrophy. Here, we discuss how native formaldehyde assimilation pathways can additionally be employed as a premise to achieving synthetic methylotrophy. Lastly, we discuss how emerging knowledge on regulation of formaldehyde metabolism can contribute to creating synthetic regulatory circuits applied in metabolic engineering strategies.

Determination of catechin and glutathione using copper aspartate nanofibers with multiple enzyme-like activities

Copper aspartate nanofibers were facilely prepared based on aspartic acid and copper (CuAsp nanofibers). It is found that the prepared CuAsp nanofibers have catalytic activities of five enzymes, including peroxidase, laccase, catalase, ascorbate oxidase, and superoxide dismutase mimetic activities. The kinetic and catalytic properties of CuAsp nanofibers were systematically investigated, showing their high catalytic activity, excellent stability, and reusability. The laccase mimetic activity of nanofibers could be used to detect catechin in the range 20-1200 µM with a detection limit of 5.88 µM. In addition, a sensing platform for glutathione with a detection limit of 0.25 µM and a detection range of 1-50 µM was established based on CuAsp nanofibers which have the peroxidase-mimicking activity. The sensor had good selectivity and could detect glutathione in actual samples of human serum. Therefore, CuAsp nanofibers with multi-enzyme activity have broad application prospects such as biosensing, environmental management, and disease diagnosis.

Fixation can change the appearance of phase separation in living cells

Fixing cells with paraformaldehyde (PFA) is an essential step in numerous biological techniques as it is thought to preserve a snapshot of biomolecular transactions in living cells. Fixed-cell imaging techniques such as immunofluorescence have been widely used to detect liquid-liquid phase separation (LLPS) in vivo. Here, we compared images, before and after fixation, of cells expressing intrinsically disordered proteins that are able to undergo LLPS. Surprisingly, we found that PFA fixation can both enhance and diminish putative LLPS behaviors. For specific proteins, fixation can even cause their droplet-like puncta to artificially appear in cells that do not have any detectable puncta in the live condition. Fixing cells in the presence of glycine, a molecule that modulates fixation rates, can reverse the fixation effect from enhancing to diminishing LLPS appearance. We further established a kinetic model of fixation in the context of dynamic protein-protein interactions. Simulations based on the model suggest that protein localization in fixed cells depends on an intricate balance of protein-protein interaction dynamics, the overall rate of fixation, and notably, the difference between fixation rates of different proteins. Consistent with simulations, live-cell single-molecule imaging experiments showed that a fast overall rate of fixation relative to protein-protein interaction dynamics can minimize fixation artifacts. Our work reveals that PFA fixation changes the appearance of LLPS from living cells, presents a caveat in studying LLPS using fixation-based methods, and suggests a mechanism underlying the fixation artifact.

Temporal control of protein labeling by photo-caged benzaldehyde motif and discovery of host cell factors of avian influenza virus infection

Photo-caged benzaldehyde probes using o-nitrophenylethylene glycol were designed for photo-activated electrophile generation. Unlike radical reaction that produce uncontrolled multiple reaction paths resulting low yield of crosslinking, reaction of electrophile has...

Flow Cytometric Analysis of Bacterial Protein Synthesis: Monitoring Vitality After Water Treatment

Bacterial vitality after water disinfection treatment was investigated using bio-orthogonal non-canonical amino acid tagging (BONCAT) and flow cytometry (FCM). Protein synthesis activity and DNA integrity (BONCAT–SYBR Green) was monitored in Escherichia coli monocultures and in natural marine samples after UV irradiation (from 25 to 200 mJ/cm²) and heat treatment (from 15 to 45 min at 55°C). UV irradiation of E. coli caused DNA degradation followed by the decrease in protein synthesis within a period of 24 h. Heat treatment affected both DNA integrity and protein synthesis immediately, with an increased effect over time. Results from the BONCAT method were compared with results from well-known methods such as plate counts (focusing on growth) and LIVE/DEAD™ BacLight™ (focusing on membrane permeability). The methods differed somewhat with respect to vitality levels detected in bacteria after the treatments, but the results were complementary and revealed that cells maintained metabolic activity and membrane integrity despite loss of cell division. Similarly, analysis of protein synthesis in marine bacteria with BONCAT displayed residual activity despite inability to grow or reproduce. Background controls (time zero blanks) prepared using different fixatives (formaldehyde, isopropanol, and acetic acid) and several different bacterial strains revealed that the BONCAT protocol still resulted in labeled, i.e., apparently active, cells. The reason for this is unclear and needs further investigation to be understood. Our results show that BONCAT and FCM can detect, enumerate, and differentiate bacterial cells after physical water treatments such as UV irradiation and heating. The method is reliable to enumerate and explore vitality of single cells, and a great advantage with BONCAT is that all proteins synthesized within cells are analyzed, compared to assays targeting specific elements such as enzyme activity.

Highly Efficient Cyclization Approach of Propargylated Peptides via Gold(I)-Mediated Sequential C-N, C-O, and C-C Bond Formation

A rapid and efficient cyclization of unprotected N-propargylated peptides using the Au(I) organometallic complex is reported. The method relies on the activation of the propargyl functionality using gold(I) to produce a new linkage with the N-terminus amine at the cyclization site. The presented method features a fast reaction rate (within 20 min), mild conditions, chemoselectivity, wide sequence scope, and high yields (up to 87%). The strategy was successfully tested on a wide variety of 30 unprotected peptides having various sequences and lengths, thus providing access to structurally distinct cyclic peptides. The practical usefulness of this method was demonstrated in producing peptides that bind efficiently to Lys48-linked di- and tetra-ubiquitin chains. The new cyclic peptide modulators exhibited high permeability to living cells and promoted apoptosis via binding with the endogenous Lys48-linked ubiquitin chains.

Translation complex stabilization on messenger RNA and footprint profiling to study the RNA responses and dynamics of protein biosynthesis in the cells

During protein biosynthesis, ribosomes bind to messenger (m)RNA, locate its protein-coding information, and translate the nucleotide triplets sequentially as codons into the corresponding sequence of amino acids, forming proteins. Non-coding mRNA features, such as 5' and 3' untranslated regions (UTRs), start sites or stop codons of different efficiency, stretches of slower or faster code and nascent polypeptide interactions can alter the translation rates transcript-wise. Most of the homeostatic and signal response pathways of the cells converge on individual mRNA control, as well as alter the global translation output. Among the multitude of approaches to study translational control, one of the most powerful is to infer the locations of translational complexes on mRNA based on the mRNA fragments protected by these complexes from endonucleolytic hydrolysis, or footprints. Translation complex profiling by high-throughput sequencing of the footprints allows to quantify the transcript-wise, as well as global, alterations of translation, and uncover the underlying control mechanisms by attributing footprint locations and sizes to different configurations of the translational complexes. The accuracy of all footprint profiling approaches critically depends on the fidelity of footprint generation and many methods have emerged to preserve certain or multiple configurations of the translational complexes, often in challenging biological material. In this review, a systematic summary of approaches to stabilize translational complexes on mRNA for footprinting is presented and major findings are discussed. Future directions of translation footprint profiling are outlined, focusing on the fidelity and accuracy of inference of the native in vivo translation complex distribution on mRNA.

Kinetics of Azanone (HNO) Reactions with Thiols: Effect of pH

HNO (nitroxyl, IUPAC name azanone) is an electrophilic reactive nitrogen species of growing pharmacological and biological significance. Here, we present data on the pH-dependent kinetics of azanone reactions with the low molecular thiols glutathione and N-acetylcysteine, as well as with important serum proteins: bovine serum albumin and human serum albumin. The competition kinetics method used is based on two parallel HNO reactions: with RSH/RS- or with O2. The results provide evidence that the reaction of azanone with the anionic form of thiols (RS-) is favored over reactions with the protonated form (RSH). The data are supported with quantum mechanical calculations. A comprehensive discussion of the HNO reaction with thiolates is provided.

Introducing Polyhydroxyurethane Hydrogels and Coatings for Formaldehyde Capture

Formaldehyde (FA) is a harmful chemical product largely used for producing resins found in our living spaces. Residual FA that leaches out the resin contributes to our indoor air pollution and causes some important health issues. Systems able to capture this volatile organic compound are highly desirable; however, traditional adsorbents are most often restricted to air filtration systems. Herein, we report novel waterborne coatings that are acting as a FA sponge for indoor air decontamination. These coatings, of the poly(hydroxyurethane) (PHU) type, rich in primary amine groups, are prepared by the polyaddition of a hydrosoluble dicyclic carbonate to a polyamine in water at room temperature under catalyst-free conditions. We highlight the importance of the choice of the polyamine on the curing rate of the formulation and on the FA capture ability of PHU. The excellent FA capturing ability of the best candidate is rationalized by investigating the action mode of the polyamine used to construct PHUs. With poly(vinyl amine), FA is covalently and permanently bound to PHU, with no release over time. The performance of the coating in FA abatement is impressive, with more than 90% of captured FA after one day of contact. The facility to prepare these transparent and colorless coatings from waterborne formulations gives access to new efficient indoor air depolluting solutions, potentially applicable to various surfaces of our living spaces (wall, ceiling, etc.).