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III–V colloidal quantum dots (QDs) promise Pb and Hg-free QD compositions with which to build short-wavelength infrared (SWIR) optoelectronic devices. However, their synthesis is limited by the availability of group-V precursors with controllable reactivities to prepare monodisperse, SWIR-absorbing III–V QDs. Here, we report a one-pot heat-up method to synthesize ∼8 nm edge length (∼6.5 nm in height) tetrahedral, SWIR-absorbing InAs QDs by increasing the [In3+]:[As3+] ratio introduced using commercially available InCl3 and AsCl3 precursors and by decreasing the concentration and optimizing the volume of the reducing reagent superhydride to control the concentration of In(0) and As(0) intermediates through QD nucleation and growth. InAs QDs are treated with NOBF4, and their deposited films are exchanged with Na2S to yield n-type InAs QD films. We realize the only colloidal InAs QD photoconductors with responsivity at the technologically important wavelength of 1.55 μm. [ABSTRACT FROM AUTHOR]

Herein, we describe a general hydrodefunctionalization protocol of alcohols and amines through a common isonitrile intermediate. To cleave the relatively inert C−NC bond, we leveraged dual hydrogen atom transfer (HAT) and photoredox catalysis to generate a nucleophilic boryl radical, which readily forms an imidoyl radical intermediate from the isonitrile. Rapid β‐scission then accomplishes defunctionalization. This method has been applied to the hydrodefunctionalization of both amine and alcohol‐containing pharmaceuticals, natural products, and biomolecules. We extended this approach to the reduction of carbonyls and olefins to their saturated counterparts, as well as the hydrodecyanation of alkyl nitriles. Both experimental and computational studies demonstrate a facile β‐scission of the imidoyl radical, and reconcile differences in reactivity between nitriles and isonitriles within our protocol. [ABSTRACT FROM AUTHOR]

Herein, we describe a general hydrodefunctionalization protocol of alcohols and amines through a common isonitrile intermediate. To cleave the relatively inert C−NC bond, we leveraged dual hydrogen atom transfer (HAT) and photoredox catalysis to generate a nucleophilic boryl radical, which readily forms an imidoyl radical intermediate from the isonitrile. Rapid β‐scission then accomplishes defunctionalization. This method has been applied to the hydrodefunctionalization of both amine and alcohol‐containing pharmaceuticals, natural products, and biomolecules. We extended this approach to the reduction of carbonyls and olefins to their saturated counterparts, as well as the hydrodecyanation of alkyl nitriles. Both experimental and computational studies demonstrate a facile β‐scission of the imidoyl radical, and reconcile differences in reactivity between nitriles and isonitriles within our protocol. [ABSTRACT FROM AUTHOR]

Hollow SiO 2 microspheres have become attractive materials for nanotechnology applications owing to their biological inertness and high functionality. In this study, hydrophobic spherical hollow cages were formed using the soft stencil method with Pluronic F127 and cetyltrimethylammonium bromide (CTAB) as the structure-directing agent, and hollow nanoporous SiO 2 microspheres (FHMS) were prepared using the soft template method. Various of amine functionalization modes were further employed to demonstrate the complexity of the relationship between pore structure/amidation mode/amine content and adsorption capacity. The hollow morphology of the porous silica was revealed using field-emission scanning electron microscopy (SEM) and transmission electron microscopy (TEM), and its porous properties were revealed using nitrogen adsorption-desorption isotherm measurements. Experiments on the fixed-bed dynamic adsorption process at 15% CO 2 showed that the high specific surface area, high pore volume and amine content of the carriers had a positive effect on the adsorption performance. However, the accessibility of the adsorption centre was affected at high loadings, and the amine efficiency and adsorption capacity were reduced. The dual amine functionalized FHMS-G-I60 maintained the integrity and order of the hollow mesoporous carrier structure, and overcame the dilemma of easy loss in the cycle process of the impregnation method and the low adsorption capacity of the grafting method. It possessed an adsorption capacity of 3.62 mmol/g, high adsorption cycling stability (more than 99.5% adsorption maintained after 10 cycles) and high amine efficiency (0.2852 mmol CO 2 /mmol N). CO 2 -TPD analysis (Thermal Programmed Desorption) further showed that FHMS-G-I60 had a faster desorption rate and lower regeneration energy consumption. In general, such structure-directed prepared matrices and functionalized with different amines are promising and low-cost adsorbents that can be used to capture CO 2 from ambient air and flue gases under different demands. [ABSTRACT FROM AUTHOR]

A new family of two‐dimensional (2D) transition metal carbides, carbonitrides, and nitrides (MXenes) has attracted increasing attention owing to their electrical, chemical, and physical properties. Together with various attractive properties of the MXenes, they also exhibit electrochemical induced deformation (i.e., expansion/contraction) via ion intercalation/de‐intercalation in/from MXene layers. In this respect, MXenes offer the possibility of application as the electrode of electrochemical actuators (ECAs). While the MXene‐based ECAs are still in their infancy stage, researchers have made great effort to achieve high‐performance MXene‐based electrochemical capacitors (ECs). As the name suggests, both ECAs and ECs shared common traits in which their operations are based on electrochemical processes. This review provides the recent progress in the MXene‐based ECAs in parallel with that in the MXene‐based ECs to gain insights from the relatively mature developments in EC applications. Finally, based on the findings from previous studies on both electrochemical applications, perspectives on future MXene‐based ECAs in terms of electrode, electrolyte, and cell configuration are provided. [ABSTRACT FROM AUTHOR]

On Earth and beyond, organic chemistry often occurs in the presence of water within environments that deviate drastically from ambient conditions (25 °C and 1 bar). Accurately predicting aqueous organic reaction pathways is crucial toward understanding planetary scale processes such as the cycling of elements crucial for life (e.g., carbon and nitrogen). Advanced thermodynamic modeling can be utilized to determine the favorability of various organic reactions based on geologically relevant ranges of temperature and pressure, as well as compositional variables (e.g., pH). However, data that would otherwise allow for a diversity of organic compounds and environmental conditions to be modeled are sparse and rarely tested with experiments, particularly with regard to organic-nitrogen compounds. In this work, we develop a framework to estimate thermodynamic properties at ambient conditions that can then be extrapolated across ranges of temperature and pressure for aqueous primary, secondary, and tertiary amines and aminiums (protonated amines), specifically those structures containing linear alkyl chains and benzyl functional groups. We also performed hydrothermal experiments (250 °C, ∼40 bar) involving reactions of methylamines to test our resulting thermodynamic models, and we compare our models for other alkylamines and benzylamines to previous empirical measurements from the literature. Specifically, we use existing thermodynamic data along with our estimates at ambient conditions in combination with a variety of existing extrapolation methods related to the revised Helgeson-Kirkham-Flowers (HKF) equations of state to generate temperature- and pressure-dependent predictions of acid dissociation constants (i.e., p K a values) that strongly agree with previous empirical measurements. We use similar methods to predict product distributions for reactions involving primary, secondary, and tertiary amines/aminiums, as well as ammonia/ammonium and corresponding alcohols whose collective distributions depend on reversible substitution reactions. Our predictions are in good agreement with our experimental results involving the methylamine reaction system as well as previous experiments involving the benzylamine reaction system, for which we also produced thermodynamic estimates involving benzyl alcohol. The agreement between independent theoretical predictions and experimental measurements suggests that our estimated properties can be applied to modeling amine chemistry in other experimental and natural aqueous systems that range in temperature and pressure, providing new tools for planetary exploration. [ABSTRACT FROM AUTHOR]

Recent developments in sequencing and bioinformatics have advanced our understanding of adenosine‐to‐inosine (A‐to‐I) RNA editing. Surprisingly, recent analyses have revealed the capability of adenosine deaminase acting on RNA (ADAR) to edit DNA:RNA hybrid strands. However, edited inosines in DNA remain largely unexplored. A precise biochemical method could help uncover these potentially rare DNA editing sites. We explore maleimide as a scaffold for inosine labeling. With fluorophore‐conjugated maleimide, we were able to label inosine in RNA or DNA. Moreover, with biotin‐conjugated maleimide, we purified RNA and DNA containing inosine. Our novel technique of inosine chemical labeling and affinity molecular purification offers substantial advantages and provides a versatile platform for further discovery of A‐to‐I editing sites in RNA and DNA. [ABSTRACT FROM AUTHOR]

BRAF mutation identification is important for the diagnosis and treatment of several tumor types, both solid and hematologic. Rapid identification of BRAF mutations is required to determine eligibility for targeted BRAF inhibitor therapy. The Idylla BRAF mutation assay is a rapid, multiplex allele-specific PCR test designed to detect the most common oncogenic BRAF V600 mutations in formalin-fixed paraffin-embedded (FFPE) tissue samples. Here, we describe the validation of the Idylla BRAF mutation assay in our laboratory. During routine clinical practice, we noticed cases in which BRAF V600 mutations were identified with unusual amplification curves, with three cases displaying a delayed amplification within a double amplification pattern and two false-positive calls. We therefore initiated a quality improvement effort to systematically and retrospectively evaluate next-generation sequencing (NGS)-tested cases with BRAF mutations identified within five amino acids of BRAF codon V600 and did not identify additional false-positive cases. We hypothesize that late amplification in a double amplification pattern may represent non-specific amplification, whereas cases displaying single delayed amplification curves may stem from the presence of either non-V600 variants, very low-level V600 variants, cytosine deamination artifacts, and/or non-specific amplification by an allele-specific PCR primer. Regardless, we recommend that Idylla BRAF cases with non-classical amplification curves undergo reflex NGS testing. These findings are likely relevant for other Idylla assays interrogating hotspot mutations in genes such as EGFR, IDH1/2, KRAS, and NRAS. [ABSTRACT FROM AUTHOR]

BACKGROUND: Enzymatic modification is an effective means of improving the functional properties, digestive properties, and in vitro digestion product physiological activity of proteins, thus significantly expanding protein uses in various food applications. RESULTS: In this study, the addition of chymotrypsin (CT) at pH 9.0 and 11.0 was found to significantly improve the functional properties (solubility, foaming properties, water holding capacity, oil holding capacity, etc.) and digestive properties of extruded corn gluten meal (ECGM). Similar changes were observed when treating ECGM with glutaminase, protein glutaminase, and papain. These changes were likely due to the increase in number of carboxyl groups and the multiple effects of change in protein net charge and conformation caused by enzymatic deamidation. Of note, ECGM deamidated by CT showed the highest degree of deamidation, solubility, and gastrointestinal digestibility at pH 11.0, up to 44.92%, 43.75%, and 82.22%, respectively. In addition, CT‐ECGM digestion product exhibited strong antioxidant activity and potential to promote alcohol metabolism in both a static digestion model and dynamic digestion model, even comparable to commercial corn peptides (CCP), while being inexpensive and of low bitterness compared to CCP. Meanwhile, the physiological activity enhanced as the molecular weight of digestion product decreased with the digested component having strongest activity. CONCLUSION: This study may promote the application of ECGM as a food component in the food industry or even as a substitute for CCP. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

The influence of conditions on the course of the reactions between 1,2-diaminoimidazole and N-arylmaleimides was studied. It was shown that, depending on the reaction conditions used, 10-amino-N-aryl-2-oxo-2,3,4,10-tetrahydropyrimido[1,2-a]benzimidazole-4-carboxamides or their deamination products, N-aryl-2-oxo-1,2,3,4-tetrahydropyrimido[1,2-a]benzimidazole-4-carboxamides, were formed. Virtual screening and molecular docking of this class of compounds allowed us to consider them as potential CRF1 receptor antagonists. [ABSTRACT FROM AUTHOR]

S-Adenosyl-l-homocysteine hydrolase (SAHH) reversibly cleaves S-adenosyl-l-homocysteine, the product of S-adenosyl-l-methionine-dependent methylation reactions. The conversion of S-adenosyl-l-homocysteine into adenosine and l-homocysteine plays an important role in the regulation of the methyl cycle. An alternative metabolic route for S-adenosyl-l-methionine regeneration in the extremophiles Methanocaldococcus jannaschii and Thermotoga maritima has been identified, featuring the deamination of S-adenosyl-l-homocysteine to S-inosyl-l-homocysteine. Herein, we report the structural characterisation of different archaeal SAHHs together with a biochemical analysis of various SAHHs from all three domains of life. Homologues deriving from the Euryarchaeota phylum show a higher conversion rate with S-inosyl-l-homocysteine compared to S-adenosyl-l-homocysteine. Crystal structures of SAHH originating from Pyrococcus furiosus in complex with SlH and inosine as ligands, show architectural flexibility in the active site and offer deeper insights into the binding mode of hypoxanthine-containing substrates. Altogether, the findings of our study support the understanding of an alternative metabolic route for S-adenosyl-l-methionine and offer insights into the evolutionary progression and diversification of SAHHs involved in methyl and purine salvage pathways. The biochemical characterisation of S-adenosyl-l-homocysteine hydrolases from all three domains of life supports the assumption that alternative routes for methyl metabolism coupled to purine salvage exist in some classes of Euryarchaeota. [ABSTRACT FROM AUTHOR]

BACKGROUND: Wheat gluten (WG) containing gliadin and glutenin are considered the main allergens in wheat allergy as a result of their glutamine‐rich peptides. Deamidation is a viable and efficient approach for protein modifications converting glutamine into glutamic acid, which may have the potential for allergenicity reduction of WG. RESULTS: Deamidation by citric acid was performed to investigate the effects on structure, allergenicity and noodle textural properties of wheat gluten (WG). WG was heated at 100 °C in 1 m citric acid to yield deamidated WG with degrees of deamidation (DD) ranging from DWG‐25 (25% DD) to DWG‐70 (70% DD). Fourier‐transform infrared and intrinsic fluorescence spectroscopy results suggested the unfolding of WG structure during deamidation, and sodium dodecyl sulphate‐polyacrylamide gel electrophoresis showed molecular weight shifts at the 35–63 kDa region, suggesting that the deamidation mainly occurred on low molecular weight glutenin subunits and γ‐ gliadin of the WG. An enzyme‐linked immunosorbent assay of deamidated WG revealed a decrease in absorbance and immunoblotting indicated that the intensities of protein bands at 35–63 kDa decreased, which suggested that deamidation of WG might have caused a greater loss of epitopes than the generation of new epitopes caused by unfolding of WG, and thereby reduction of the immunodominant immunoglobulin E binding capacity, ultimately leading to the decrease in allergenicity. DWG‐25 was used in the preparation of recombinant hypoallergenic noodles, and the hardness, elasticity, chewiness and gumminess were improved significantly by the addition of azodicarbonamide. CONCLUSION: The present shows the potential for deamidation of the WG products used in novel hypoallergenic food development. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

Antibody-based therapeutics must not undergo chemical modifications that would impair their efficacy or hinder their developability. A commonly used technique to de-risk lead biotherapeutic candidates annotates chemical liability motifs on their sequence. By analyzing sequences from all major sources of data (therapeutics, patents, GenBank, literature, and next-generation sequencing outputs), we find that almost all antibodies contain an average of 3–4 such liability motifs in their paratopes, irrespective of the source dataset. This is in line with the common wisdom that liability motif annotation is over-predictive. Therefore, we have compiled three computational flags to prioritize liability motifs for removal from lead drug candidates: 1. germline, to reflect naturally occurring motifs, 2. therapeutic, reflecting chemical liability motifs found in therapeutic antibodies, and 3. surface, indicative of structural accessibility for chemical modification. We show that these flags annotate approximately 60% of liability motifs as benign, that is, the flagged liabilities have a smaller probability of undergoing degradation as benchmarked on two experimental datasets covering deamidation, isomerization, and oxidation. We combined the liability detection and flags into a tool called Liability Antibody Profiler (LAP), publicly available at lap.naturalantibody.com. We anticipate that LAP will save time and effort in de-risking therapeutic molecules. [ABSTRACT FROM AUTHOR]

Selective cleavage of unstrained (sp3) C−C/ C−N bonds under mild conditions is highly challenging due to the higher bond dissociation energy. A visible light mediated metal‐free oxidative dehomologation of aryl acetonitriles, primary alcohols and diols to carboxylic acids via organophotocatalyzed C(sp3)−CN, C(sp3)−C(OH) bond cleavage is reported. Notably, this methodology was further extended towards selective synthesis of aldehydes via deamination of both primary as well as secondary amines. This mild protocol features wide array of substrate variation with excellent functional group tolerance, preparative‐scale synthesis, and operational simplicity. Possible mechanisms for these transformations were demonstrated through a series of control experiments. [ABSTRACT FROM AUTHOR]

A facile one‐pot microwave‐assisted synthesis of pyrazolopyrimidines and pyrazolothiazoles was developed by reacting 5‐amino‐4‐thiocyanato‐pyrazoles with Vilsmeier Reagent (PBr3/foramide). The reaction gave the corresponding pyrazolopyrimidines as major products in good yields (61–85 %) and pyrazolothiazoles as minor products (11–23 % yields). The plausible reaction mechanism was proposed to account for the transformation of pyrazolopyrimidines and pyrazolothiazoles through two paths A and B. In path A, the reaction leading to the formation of pyrazolopyrimidines proceeded through four sequential steps, including acidic catalyzed cascade dethiocyanation/cyclization, Vilsmeier reaction, ring expansion, and deamination. The formation of the pyrazolothiazole in path B was caused by the nucleophilic heterocyclization reaction involving the sulfur nucleophilic reaction of thiocyanate (R−SC≡N) and the departure of a cyanamide. Based on the experimental results, we observed that the path A for the formation of pyrazolopyrimidines was more favorable. [ABSTRACT FROM AUTHOR]

The introduction of trifluoromethyl groups into organic molecules is of paramount importance in modern synthetic chemistry and medicinal chemistry. While methods for constructing C(sp2)−CF3 bonds have been well established, the advancement of practical and comprehensive approaches for forming C(sp3)−CF3 bonds remains considerably restricted. In this work, we describe an efficient and site‐specific deaminative trifluoromethylation reaction of aliphatic primary amines to afford the corresponding alkyl trifluoromethyl compounds. The reaction proceeds at room temperature with readily accessible N‐anomeric amide (Levin's reagent) and bench‐stable bpyCu(CF3)3 (Grushin's reagent, bpy=2,2′‐bipyridine) under blue light. The protocol features mild reaction conditions, good functional group tolerance, and moderate to good yields. Remarkably, the method can be applied to the direct, late‐stage trifluoromethylation of natural products and bioactive molecules. Experimental mechanistic studies were conducted, and a radical mechanism is proposed, wherein the dual roles of Grushin's reagent have been elucidated. [ABSTRACT FROM AUTHOR]

The introduction of trifluoromethyl groups into organic molecules is of paramount importance in modern synthetic chemistry and medicinal chemistry. While methods for constructing C(sp2)−CF3 bonds have been well established, the advancement of practical and comprehensive approaches for forming C(sp3)−CF3 bonds remains considerably restricted. In this work, we describe an efficient and site‐specific deaminative trifluoromethylation reaction of aliphatic primary amines to afford the corresponding alkyl trifluoromethyl compounds. The reaction proceeds at room temperature with readily accessible N‐anomeric amide (Levin's reagent) and bench‐stable bpyCu(CF3)3 (Grushin's reagent, bpy=2,2′‐bipyridine) under blue light. The protocol features mild reaction conditions, good functional group tolerance, and moderate to good yields. Remarkably, the method can be applied to the direct, late‐stage trifluoromethylation of natural products and bioactive molecules. Experimental mechanistic studies were conducted, and a radical mechanism is proposed, wherein the dual roles of Grushin's reagent have been elucidated. [ABSTRACT FROM AUTHOR]

The photocyclization of diarylethenes toward polycyclic aromatic hydrocarbons and analogs has been well‐documented. However, stiff‐stilbene was reported to be inactive, and examples of photocyclization‐induced deamination remain unknown. Here, we report that ortho‐(N,N‐dimethylamino)‐stiff‐stilbene (1a) undergoes efficient photocyclization‐induced deamination, forming the dicyclopenta‐fused phenanthrene (DCPP) with good yield (65%) under anaerobic conditions. The relative reactivities of stiff‐stilbenes with different o‐amino substituents (1b–1g) or with an o‐methoxy (1h) group, and those of o‐(N,N‐dimethylamino)stilbenes (2a and 2aMe), provide insights into the substituent and structural effects. [ABSTRACT FROM AUTHOR]

Noncoding mutation hotspots have been identified in melanoma and many of them occur at the binding sites of E26 transformation-specific (ETS) proteins; however, their formation mechanism and functional impacts are not fully understood. Here, we used UV (Ultraviolet) damage sequencing data and analyzed cyclobutane pyrimidine dimer (CPD) formation, DNA repair, and CPD deamination in human cells at single-nucleotide resolution. Our data show prominent CPD hotspots immediately after UV irradiation at ETS binding sites, particularly at sites with a conserved TTCCGG motif, which correlate with mutation hotspots identified in cutaneous melanoma. Additionally, CPDs are repaired slower at ETS binding sites than in flanking DNA. Cytosine deamination in CPDs to uracil is suggested as an important step for UV mutagenesis. However, we found that CPD deamination is significantly suppressed at ETS binding sites, particularly for the CPD hotspot on the 5' side of the ETS motif, arguing against a role for CPD deamination in promoting ETS-associated UV mutations. Finally, we analyzed a subset of frequently mutated promoters, including the ribosomal protein genes RPL13A and RPS20, and found that mutations in the ETS motif can significantly reduce the promoter activity. Thus, our data identify high UV damage and low repair, but not CPD deamination, as the main mechanism for ETS-associated mutations in melanoma and uncover important roles of often-overlooked mutation hotspots in perturbing gene transcription. [ABSTRACT FROM AUTHOR]

It has been proposed that antidiabetic drugs, such as metformin and imatinib, at least in part, promote improved glucose tolerance in type 2 diabetic patients via increased production of the inflammatory cytokine GDF15. This is supported by studies, performed in rodent cell lines and mouse models, in which the addition or production of GDF15 improved beta-cell function and survival. The aim of the present study was to determine whether human beta cells produce GDF15 in response to antidiabetic drugs and, if so, to further elucidate the mechanisms by which GDF15 modulates the function and survival of such cells. The effects and expression of GDF15 were analyzed in human insulin-producing EndoC-betaH1 cells and human islets. We observed that alpha and beta cells exhibit considerable heterogeneity in GDF15 immuno-positivity. The predominant form of GDF15 present in islet and EndoC-betaH1 cells was pro-GDF15. Imatinib, but not metformin, increased pro-GDF15 levels in EndoC-betaH1 cells. Under basal conditions, exogenous GDF15 increased human islet oxygen consumption rates. In EndoC-betaH1 cells and human islets, exogenous GDF15 partially ameliorated cytokine- or palmitate + high-glucose-induced loss of function and viability. GDF15-induced cell survival was paralleled by increased inosine levels, suggesting a more efficient disposal of intracellular adenosine. Knockdown of adenosine deaminase, the enzyme that converts adenosine to inosine, resulted in lowered inosine levels and loss of protection against cytokine- or palmitate + high-glucose-induced cell death. It is concluded that imatinib-induced GDF15 production may protect human beta cells partially against inflammatory and metabolic stress. Furthermore, it is possible that the GDF15-mediated activation of adenosine deaminase and the increased disposal of intracellular adenosine participate in protection against beta-cell death. [ABSTRACT FROM AUTHOR]

Methylenedianiline (MDA) is a secondary, undesired, product of the glycolysis process of polyurethane (PU) scraps due to hydrolysis and pyrolysis side reactions. As an aromatic and carcinogen amine, MDA poses different problems in handling, transporting, and labelling recycled polyols derived from glycolysis, hindering the closure of PU recycling loop. Aiming to provide a solution to this issue, in this work different deaminating agents (DAs) were investigated with the purpose of analyzing their reactivity with MDA. A first part of the study was devoted to the analysis of MDA formation as a function of reaction time and catalyst concentration (potassium acetate) during glycolysis. It was observed that the amount of MDA increases almost linearly with the extent of PU depolymerization and catalyst content. Among the DAs analyzed 2‐ethylhexyl glycidyl ether (2‐EHGE), and acetic anhydride (Ac2O) showed interesting performance, which allowed MDA content to be diminished below the limit for labelling prescription in 30 minutes. PU rigid foams were, therefore, synthesized from the corresponding recycled products and characterized in terms of thermal and mechanical performance. Ac2O‐deaminated polyols led to structurally unstable foams with poor compressive strength, while 2‐EHGE‐deaminated products allowed the production of foams with improved mechanical performance and unaltered thermal conductivity. [ABSTRACT FROM AUTHOR]

The jet impact‐negative pressure deamination reactor (JI‐NPDR) is a new type of continuous and efficient deamination equipment. The study of the random flow pattern of porous jet impingement in the reactor under negative pressure conditions is an important issue. In this work, the signal processing method based on wavelet transform is used to analyze the characteristics of random flow signals in the reactor. Meanwhile, an analog similar signal is built and three sets of Gaussian white noise with various signal‐to‐noise ratios are employed via the MATLAB platform. Based on the adjustment of threshold function, threshold, decomposition level and other parameters of wavelet transform, the noise ratio (SNR) and mean squared error (MSE) are used to evaluate the wavelet denoising effect. And then, the optimal denoising scheme for the obtained signal will be applied in processing the vacuum flow signal collected inside the deamination reactor. Subsequently, the 8‐layer wavelet decomposition is investigated by using sym7 as the wavelet basis, soft threshold function, and heursure threshold for signal denoising. Then, the analog signal is fed back through the results of the actual signal denoising, and the number of wavelet decomposition layers is adjusted from 8 to 9 layers to optimize the original wavelet denoising combination. By analyzing the low‐frequency and high‐frequency parts of the signal spectrum before and after denoising, it was found that wavelet transform can effectively denoise the fluid signal in the reactor. [ABSTRACT FROM AUTHOR]

Wheat gluten protein (WGP) is a fine-quality plant-based protein resource. However, as its unparalleled reticulation structure, the processing properties of WGP are extremely poor, limiting its application. To overcome these drawbacks, the purpose of this work was to embellish wheat gluten protein by three relatively novel and mainstream chemical modifications. The results showed the pH-shifting treatment altered the apparent morphology of protein, showing a uniform flocculent structure, leading to significant improvements in foaming capacity and emulsification property. After deamidation by acetic acid, the solubility of WGP was greatly improved (60.1%), which was nearly four times that of the control group (15.8%), and its foam stability was also significantly improved. The WGP had the highest thermal stability (deformation temperature up to 148 ℃) after TGase deamidation. These results indicate that the three modification methods enhance the functional characters of WGP in different aspects and expand its application potential. [ABSTRACT FROM AUTHOR]

Photochemical reductive deamination of alpha-amino aryl alkyl ketones under photosensitizer-free conditions is presented. This protocol features high efficiency and selectivity. A plausible reaction pathway is proposed based on ultraviolet–visible absorption investigation, control experiments and deuterium-labelling studies. Mechanistic study reveals that the alpha-hydrogen atom of the ketone product originated from water. [ABSTRACT FROM AUTHOR]

Asparagine deamidation is a post-translational modification (PTM) that converts asparagine residues into iso-aspartate and/or aspartate. Non-enzymatic asparagine deamidation is observed frequently during the manufacturing, processing, and/or storage of biotherapeutic proteins. Depending on the site of deamidation, this PTM can significantly impact the therapeutic's potency, stability, and/or immunogenicity. Thus, deamidation is routinely monitored as a potential critical quality attribute. The initial evaluation of an asparagine's potential to deamidate begins with identifying sequence liabilities, in which the n + 1 amino acid is of particular interest. NW is one motif that occurs frequently within the complementarity-determining region (CDR) of therapeutic antibodies, but according to the published literature, has a very low risk of deamidating. Here we report an unusual case of this NW motif readily deamidating within the CDR of an antibody drug conjugate (ADC), which greatly impacts the ADC's biological activities. Furthermore, this NW motif solely deamidates into iso-aspartate, rather than the typical mixture of iso-aspartate and aspartate. Interestingly, biological activities are more severely impacted by the conversion of asparagine into iso-aspartate via deamidation than by conversion into aspartate via mutagenesis. Here, we detail the discovery of this unusual NW deamidation occurrence, characterize its impact on biological activities, and utilize structural data and modeling to explain why conversion to iso-aspartate is favored and impacts biological activities more severely. [ABSTRACT FROM AUTHOR]

Deamidation, a common post-translational modification, may impact multiple physiochemical properties of a therapeutic protein. MEDI7247, a pyrrolobenzodiazepine (PBD) antibody–drug conjugate (ADC), contains a unique deamidation site, N102, located within the complementarity-determining region (CDR), impacting the affinity of MEDI7247 to its target. Therefore, it was necessary to monitor MEDI7247 deamidation status in vivo. Due to the low dose, a sensitive absolute quantification method using immunocapture coupled with liquid chromatography–tandem mass spectrometry (LBA-LC-MS/MS) was developed and qualified. We characterized the isomerization via Electron-Activated Dissociation (EAD), revealing that deamidation resulted in iso-aspartic acid. The absolute quantification of deamidation requires careful assay optimization in order not to perturb the balance of the deamidated and nondeamidated forms. Moreover, the selection of capture reagents essential for the correct quantitative assessment of deamidation was evaluated. The final assay was qualified with 50 ng/mL LLOQ for ADC for total and nondeamidated antibody quantification, with qualitative monitoring of the deamidated antibody. The impact of deamidation on the pharmacokinetic characteristics of MEDI7247 from clinical trial NCT03106428 was analyzed, revealing a gradual reduction in the nondeamidated form of MEDI7247 in vivo. Careful quantitative biotransformation analyses of complex biotherapeutic conjugates help us understand changes in product PTMs after administration, thus providing a more complete view of in vivo pharmacology. [ABSTRACT FROM AUTHOR]

Rhamnolipid, as a low‐toxic, biodegradable and environmentally friendly biosurfactant, has broad application prospects in many industries. However, the quantitative determination of rhamnolipid is still a challenging task. Here, a new sensitive method for the quantitative analysis of rhamnolipid based on a simple derivatization reaction was developed. In this study, 3‐[3′‐(l‐rhamnopyranosyloxy) decanoyloxy] decanoic acid (Rha‐C10‐C10) and 3‐[3′‐(2′‐O‐α‐l‐rhamnopyranosyloxy) decanoyloxy] decanoic acid (Rha‐Rha‐C10‐C10) were utilized as the representative rhamnolipids. Liquid chromatography–mass spectrometry and high‐performance liquid chromatography‐ultra violet results showed that these two compounds were successfully labeled with 1 N1‐(4‐nitrophenyl)‐1,2‐ethylenediamine. There was an excellent linear relationship between rhamnolipid concentration and peak area of labeled rhamnolipid. The detection limits of the Rha‐C10‐C10 and Rha‐Rha‐C10‐C10 were 0.018 mg/L (36 nmol/L) and 0.014 mg/L (22 nmol/L), respectively. The established amidation method was suitable for the accurate analysis of rhamnolipids in the biotechnological process. The method had good reproducibility with the relative standard deviation of 0.96% and 0.79%, respectively, and sufficient accuracy with a recovery of 96%–100%. This method was applied to quantitative analysis of 10 rhamnolipid homologs metabolized by Pseudomonas aeruginosa LJ‐8. The single labeling method was used for the quantitative analysis of multiple components, which provided an effective method for the quality evaluation of other glycolipids with carboxyl groups. [ABSTRACT FROM AUTHOR]

Metal corrosion poses a substantial economic challenge in a technologically advanced world. In this study, novel environmentally friendly anticorrosive graphene oxide (GO)-doped organic-inorganic hybrid polyurethane (LFAOIH@GO-PU) nanocomposite coatings were developed from Leucaena leucocephala oil (LLO). The formulation was produced by the amidation reaction of LLO to form diol fatty amide followed by the reaction of tetraethoxysilane (TEOS) and a dispersion of GOx (X = 0.25, 0.50, and 0.75 wt%) along with the reaction of isophorane diisocyanate (IPDI) (25–40 wt%) to form LFAOIH@GOx-PU35 nanocomposites. The synthesized materials were characterized by Fourier transform infrared spectroscopy (FTIR); 1H, 13C, and 29Si nuclear magnetic resonance; and X-ray photoelectron spectroscopy. A detailed examination of LFAOIH@GO0.5-PU35 morphology was conducted using X-ray diffraction, scanning electron microscopy, energy-dispersive X-ray spectroscopy, and transmission electron microscopy. These studies revealed distinctive surface roughness features along with a contact angle of around 88 G.U preserving their structural integrity at temperatures of up to 235 °C with minimal loading of GO. Additionally, improved mechanical properties, including scratch hardness (3 kg), pencil hardness (5H), impact resistance, bending, gloss value (79), crosshatch adhesion, and thickness were evaluated with the dispersion of GO. Electrochemical corrosion studies, involving Nyquist, Bode, and Tafel plots, provided clear evidence of the outstanding anticorrosion performance of the coatings. [ABSTRACT FROM AUTHOR]

The reaction of triflamide with allyl cyanide in benzonitrile and isobutyronitrile solutions in the presence of NBS has been studied. In both cases, the corresponding amidines formed by solvent insetion were obtained. In benzonitrile, depending on the reaction conditions, the isomeric N-(2-bromo-3-cyanopropyl)-N'-(triflyl)benzamidine and N-(1-bromo-3-cyanoprop-2-yl)-N'-(triflyl)benzamidine were obtained in various ratios. The reaction in isobutyronitrile resulted in the isolation of N-(2-bromo-3-cyanopropyl)-N'-(triflyl)isobutyramidine and the deamination product N-[3-cyano-1-(triflamido)propyl]isobutyramide. [ABSTRACT FROM AUTHOR]

Highly efficient recycling of carbon fiber reinforced polymer composites into monomers and fibers is a formidable challenge. Herein, we present a closed‐loop recycling approach for carbon fiber reinforced polymer composites using reversible amidation chemistry, which enables the complete recovery of intact carbon fibers and pure monomers. The polymer network, synthesized by amidation between a macromonomer linear polyethyleneimine and a bifunctional maleic anhydride cross‐linker, serves as a matrix for the construction of composites with exceptional mechanical properties, thermal stability and solvent resistance. The matrices can be fully depolymerized under the acidic condition at ambient temperature, allowing the effective separation and recovery of both carbon fibers and the two monomers. The reclaimed carbon fibers retain nearly identical mechanical properties to pristine ones, while pure monomers are recycled with high separation yields (>93 %). They can be reused in for multiple cycles for the manufacture of new composites, whose mechanical properties recover over 95 % of their original properties. This line of research presents a promising approach for the design of high‐performance and sustainable thermoset composites, offering significant environmental and economic benefits. [ABSTRACT FROM AUTHOR]

Highly efficient recycling of carbon fiber reinforced polymer composites into monomers and fibers is a formidable challenge. Herein, we present a closed‐loop recycling approach for carbon fiber reinforced polymer composites using reversible amidation chemistry, which enables the complete recovery of intact carbon fibers and pure monomers. The polymer network, synthesized by amidation between a macromonomer linear polyethyleneimine and a bifunctional maleic anhydride cross‐linker, serves as a matrix for the construction of composites with exceptional mechanical properties, thermal stability and solvent resistance. The matrices can be fully depolymerized under the acidic condition at ambient temperature, allowing the effective separation and recovery of both carbon fibers and the two monomers. The reclaimed carbon fibers retain nearly identical mechanical properties to pristine ones, while pure monomers are recycled with high separation yields (>93 %). They can be reused in for multiple cycles for the manufacture of new composites, whose mechanical properties recover over 95 % of their original properties. This line of research presents a promising approach for the design of high‐performance and sustainable thermoset composites, offering significant environmental and economic benefits. [ABSTRACT FROM AUTHOR]

Charge variants, as an important quality attribute of mAbs, must be comprehensively characterized and monitored during development. However, due to their complex structure, the characterization of charge variants is challenging, labor-intensive, and time-consuming when using traditional approaches. This work combines on-line and off-line 2D-LC-MS to comprehensively characterize mAb charge variants and quickly offer precise instructions for process development. Six charge variant peaks of mAb 1 were identified using the developed platform. Off-line 2D-LC-MS analysis at the peptide level showed that the acidic peak P1 and the basic peaks P4 and P5 were caused by the deamidation of asparagine, the oxidation of methionine, and incomplete C-terminal K loss, respectively. On-line 2D-LC-MS at the intact protein level was used to identify the root causes, and it was found that the acidic peak P2 and the basic peak P6 were due to the glutathionylation of cysteine and succinimidation of aspartic acid, respectively, which were not found in off-line 2D-LC-MS because of the loss occurring during pre-treatment. These results suggest that process development could focus on cell culture for adjustment of glutathionylation. In this paper, we propose the concept of precision process development based on on-line 2D-LC-MS, which could quickly offer useful data with only 0.6 mg mAb within 6 h for precise instructions for process development. Overall, the combination of on-line and off-line 2D-LC-MS can characterize mAb charge variants more comprehensively, precisely, and quickly than other approaches. This is a very effective platform with routine operations that provides precise instructions for process development within hours, and will help to accelerate the development of innovative therapeutics. [ABSTRACT FROM AUTHOR]

This review is intended to elucidate the structure, biological activity, and use of various strategies for the synthesis of terphenyl and its derivatives from amines obtained by the Stevens rearrangement. The amine transformation is a domino reaction, including β-elimination of secondary amine with the formation of a conjugated dienyne, which forms a cyclic allene intermediate by an electrocyclic reaction. The subsequent 1,3- or 1,5-hydride shift rapidly produces the final compound. [ABSTRACT FROM AUTHOR]

ω-transaminase has attracted growing attention for chiral amine synthesis, although it commonly suffers from severe by-product inhibition. ω-transaminase CrmG is critical for the biosynthesis of Caerulomycin A, a natural product that possesses broad bioactivity, including immunosuppressive and anti-cancer. Compared to L-Arg, amino donor L-Glu, L-Gln or L-Ala is more preferred by CrmG. In this study, we determined the crystal structure of CrmG in complex with amino donor L-Arg, unveiling the detailed binding mode. Specifically, L-Arg exhibits an extensive contact with aromatic residues F207 and W223 on the roof of CrmG active site via cation-π network. This interaction may render the deamination by-product of L-Arg to be an inhibitor against PMP-bound CrmG by stabilizing its flexible roof, thus reducing the reactivity of L-Arg as an amino donor for CrmG. These data provide further evidence to support our previous proposal that CrmG can overcome inhibition from those by-products that are not able to stabilize the flexible roof of active site in PMP-bound CrmG. Thus, our result can not only facilitate the biosynthesis of CRM A but also be beneficial for the rational design of ω-transaminase to bypass by-product inhibition. • Crystal structure of CrmG in complex with amino donor L-Arg is reported. • L-Arg interacts with the roof of CrmG active site via unique cation-π network. • The interaction with the roof impairs reactive efficiency of L-Arg as CrmG amino donor. [ABSTRACT FROM AUTHOR]

For successful vector-based gene therapy manufacturing, the selected adeno-associated virus (AAV) vector production system must produce vector at sufficient scale. However, concerns have arisen regarding the quality of vector produced using different systems. In this study, we compared AAV serotypes 1, 8, and 9 produced by two different systems (Sf9/baculovirus and HEK293/transfection) and purified by two separate processes. We evaluated capsid properties, including protein composition, post-translational modification, particle content profiles, and in vitro and in vivo vector potency. Vectors produced in the Sf9/baculovirus system displayed reduced incorporation of viral protein 1 and 2 into the capsid, increased capsid protein deamidation, increased empty and partially packaged particles in vector preparations, and an overall reduced potency. The differences observed were largely independent of the harvest method and purification process. These findings illustrate the need for careful consideration when choosing an AAV vector production system for clinical production. [ABSTRACT FROM AUTHOR]

To prepare a reliable method for predicting the properties of devulcanized rubbers a nitrile rubber (NBR) compound was prepared and masticated before vulcanization for 0, 30 and 60 min under mechanical stress to prepare NBRs with different molecular weights. The masticated samples were vulcanized at different accelerator contents to prepare damples with different crosslink densities. The physical/mechanical/thermal properties (i.e. crosslink density, tensile strength, modulus, modulus at 100 and 300% elongation, elongation at break, hardness, curing behavior and molecular weight) of the samples were experimentally evaluated. In the next step, the prepared samples were assumed as devulcanized NBRs that underwent chains scission (masticated samples) or crosslinks breakage (vulcanized at different accelerator contents). On this basis, hypothetical devulcanization routes were considered between each sample that underwent chains scission or crosslinks breakage. Based on the results, numerical relationships between the number of chains scission or crosslinks breakage and decrease in the properties were obtained. Finally, the numerical reationships were used to calculate the properties of the samples that underwent both of chains scission and crosslinks breakage. It was found that the calculated contents of hardness, modulus at 100% and molecular weight (MZ) using the prepared method were very close to the evaluated ones. [ABSTRACT FROM AUTHOR]

Base excision repair (BER) corrects forms of oxidative, deamination, alkylation, and abasic single-base damage that appear to have minimal effects on the helix. Since its discovery in 1974, the field has grown in several facets: mechanisms, biology and physiology, understanding deficiencies and human disease, and using BER genes as potential inhibitory targets to develop therapeutics. Within its segregation of short nucleotide (SN-) and long patch (LP-), there are currently six known global mechanisms, with emerging work in transcription- and replication-associated BER. Knockouts (KOs) of BER genes in mouse models showed that single glycosylase knockout had minimal phenotypic impact, but the effects were clearly seen in double knockouts. However, KOs of downstream enzymes showed critical impact on the health and survival of mice. BER gene deficiency contributes to cancer, inflammation, aging, and neurodegenerative disorders. Medicinal targets are being developed for single or combinatorial therapies, but only PARP and APE1 have yet to reach the clinical stage. [ABSTRACT FROM AUTHOR]

Functionalization of single‐walled carbon nanotubes (SWCNTs) has attracted interest because it alters the near‐infrared (NIR) photoluminescence (PL) wavelength and emission efficiency. These modifications depend on the binding configuration and degree of functionalization. Excessive functionalization reduces the emission efficiency as the integrity of the conjugated π system decreases; thus, controlling the degree of functionalization is essential. Because the binding configurations and degree of functionalization are affected by the reagent structure, a stepwise approach combining SWCNTs functionalization and subsequent reactions to introduce functional groups into the addenda could effectively control their PL properties and functionalities. We studied this approach by implementing the reductive alkylation of SWCNTs by using bromoalkanes with t‐butyl carbamate (Boc)‐protected amino groups and subsequent deprotection and amidation reactions. The reaction products were analyzed based on absorption, PL, and Raman spectroscopy and the Kaiser test. Depending on the structure of the reagent, deprotection and amidation reactions competed with the elimination reaction of addenda, altering the PL properties of the SWCNTs. Furthermore, the elimination reaction was inhibited in the adducts functionalized using dibromoalkane with Boc‐protected amino groups, demonstrating that the use of appropriate reagents enables the molecular conversion of the functional groups of SWCNT adducts without affecting their PL properties. [ABSTRACT FROM AUTHOR]

Background: In this paper, wheat gluten (WG) was modified by electrochemical deamidation. The effects of electrochemical treatment time on the conformation and functional properties of WG and its mechanism were studied. Results: Wheat gluten demonstrated a maximum deamidation of 50.94%. Fourier transform infrared spectroscopy (FTIR) showed a decrease in α‐helix and β‐sheets and an increase in β‐turns and random coils, indicating that the secondary structure of WG became looser and more disordered with increased molecular flexibility. Electrochemical deamidation significantly increased the net charge and solubility of WG, the emulsifying activity index (EAI) increased from 8.53 to 15.66 m2 g−1, the foaming capacity (FC) increased from 4.55 to 13.72 cm3, and the water‐holding capacity (WHC) and oil‐holding capacity (OHC) reached maximum levels of 8.42 g g−1 and 7.45 g g−1, respectively, at 90 min. Conclusion: Electrochemical deamidation appears to be a useful technique to improve the processing characteristics of WG. © 2023 Society of Chemical Industry. [ABSTRACT FROM AUTHOR]

This study presents a novel degradation pathway of a human immunoglobulin G (IgG) molecule featuring a light chain N-terminal asparagine. We thoroughly characterize this pathway and investigate its charge profiles using cation exchange chromatography (CEX) and capillary isoelectric focusing (cIEF). Beyond the well-documented asparagine deamidation into isoaspartic acid, aspartic acid, and succinimide intermediate, a previously unreported clipping degradation pathway is uncovered. This newly identified clipped N-terminal IgG variant exhibits a delayed elution in CEX, categorized as a "basic variant", while retaining the same main peak isoelectric point (pI) in cIEF. The influence of temperature and pH on N-terminal asparagine stability is assessed across various stressed conditions. A notable correlation between deamidation percentage and clipped products is established, suggesting a potential hydrolytic chemical reaction underlying the clipping process. Furthermore, the impact of N-terminal asparagine modifications on potency is evaluated through ELISA binding assays, revealing minimal effects on binding affinity. Sequence alignment reveals homology to a human IgG with the germline gene from Immunoglobulin Lambda Variable 6-57 (IGLV6-57), which has implications for amyloid light-chain (AL) amyloidosis. This discovery of the N-terminal clipping degradation pathway contributes to our understanding of immunoglobulin light chain misfolding and amyloid fibril deposition under physiological conditions. [ABSTRACT FROM AUTHOR]

The nicotinamide adenine dinucleotide (NAD+) precursor nicotinamide mononucleotide (NMN) is a proposed therapy for age‐related disease, whereby it is assumed that NMN is incorporated into NAD+ through the canonical recycling pathway. During oral delivery, NMN is exposed to the gut microbiome, which could modify the NAD+ metabolome through enzyme activities not present in the mammalian host. We show that orally delivered NMN can undergo deamidation and incorporation in mammalian tissue via the de novo pathway, which is reduced in animals treated with antibiotics to ablate the gut microbiome. Antibiotics increased the availability of NAD+ metabolites, suggesting the microbiome could be in competition with the host for dietary NAD+ precursors. These findings highlight new interactions between NMN and the gut microbiome. [ABSTRACT FROM AUTHOR]

Increased expression of the human telomere reverse transcriptase (hTERT) in tumors promotes tumor cell survival and diminishes the survival of patients. Cytosine-to-thymine (C-to-T) transition mutations (C250T or C228T) in the hTERT promoter create binding sites for transcription factors, which enhance transcription. The G-rich strand of the hTERT promoter can form G-quadruplex structures, whereas the C-rich strand can form an i-motif in which multiple cytosine residues are protonated. We considered the possibility that i-motif formation might promote cytosine deamination to uracil and C-to-T mutations. We computationally probed the accessibility of cytosine residues in an i-motif to attack by water. We experimentally examined regions of the C-rich strand to form i-motifs using pH-dependent UV and CD spectra. We then incubated the C-rich strand with and without the G-rich complementary strand DNA under various conditions, followed by deep sequencing. Surprisingly, deamination rates did not vary substantially across the 46 cytosines examined, and the two mutation hotspots were not deamination hotspots. The appearance of mutational hotspots in tumors is more likely the result of the selection of sequences with increased promoter binding affinity and hTERT expression. [ABSTRACT FROM AUTHOR]

Oxidative deamination of benzyl amines is achieved using a Ni(II)–NHC catalyst with water in aqueous medium. The product is an aldehyde, wherein water acts as a formal oxidant. Hemilabile pyridyl units embedded in the catalyst allow the approach of amine to the metal and promotes nucleophilic water attack on the metal-bound imine. A water-soluble 3d-metal Ni(II) catalyst bearing promoter ligands opens up a new avenue for water-mediated oxidation reactions. [ABSTRACT FROM AUTHOR]

Simple Summary: Biogenic amines (BAs) originate from amino acid decarboxylation and are commonly used as markers of spoilage and putrefaction in food and feed, especially in improperly handled animal products. Detoxification of BAs occurs mainly in the intestinal tract by amine oxidases, but some factors may facilitate intestinal absorption. When consumed in high concentrations, BAs can impair colonic epithelium, intestinal functionality, and may cause other toxicological effects. This study aimed to evaluate the effects of diets based on hydrolyzed protein (hydrolyzed chicken liver powder—HCLP) or conventional intact protein (poultry by-product meal—PBPM) with increasing protein concentrations (24, 32, and 40%) on the consumption and metabolism of biogenic amines in adult dogs. The results showed that PBPM had higher concentrations of putrefactive BAs, as well as the diets with its inclusion. As a result, dogs consumed higher concentrations of putrefactive BAs with diets containing PBPM and higher protein concentrations. Despite the difference in BAs concentrations in the protein sources, there was only an increase in the fecal excretion of phenylethylamine in the HCLP32 and HCLP40 diets and the enzymatic activity of monoamine oxidase in the HCLP24 and PBPM32 diets. Our findings indicate that the inclusion of HCLP reduces the consumption of putrefactive BAs and that the BAs detoxification system is highly efficient in the intestinal tract of dogs. Biogenic amines are synthesized through the bacterial decarboxylation of amino acids, commonly found in high levels in animal by-product meals due to spoilage. Furthermore, biogenic amines and other metabolites can be produced by the fermentation of proteins in the hindgut according to the protein source and concentration of crude protein (CP) in the diet. Thus, this study aimed to evaluate two protein sources (poultry by-product meal (PBPM) and hydrolyzed chicken liver powder (HCLP)) and three CP concentrations (24, 32, and 40%) and their effects on the consumption and fecal excretion of biogenic amines, plasma monoamine oxidase (MAO) and diamine oxidase (DAO) activities, and total antioxidant capacity (TAC) of healthy adult dogs after 30 days of feeding the experimental diets. Twelve dogs were randomly distributed into six treatments (n = 6/treatment): PBPM24 (PBPM with 24% CP); PBPM32 (PBPM with 32% CP); PBPM40 (PBPM with 40% CP); HCLP24 (HCLP with 24% CP); HCLP32 (HCLP with 32% CP); HCLP40 (HCLP with 40% CP). The PBPM and PBPM-based diets had higher concentrations of putrescine, cadaverine, tyramine, histamine, agmatine, and total biogenic amines. In contrast, HCLP and HCLP-based diets contained higher concentrations of spermidine, phenylethylamine, and spermine. The PBPM and PBPM-diets had higher biogenic amine index (BAI) indicating lower quality due to the high content of putrescine, cadaverine and tyramine. Dogs fed diets with PBPM and higher protein concentrations consumed more putrescine, cadaverine, tyramine, agmatine, and total amines (p < 0.0001), while dogs fed with HCLP consumed more spermidine, phenylethylamine, and spermine (p < 0.0001). Fecal excretion of phenylethylamine was greater in dogs fed HCLP32 and HCLP40 diets (p = 0.045). Dogs fed with HCLP tended to excrete more spermidine and tryptamine via feces, while higher protein concentrations tended to increase fecal excretion of cadaverine (p < 0.10). Plasma MAO activity was higher in dogs fed HCLP24 and PBPM32 diets (p = 0.024). The plasma activities of DAO and TAC were not different between diets (p > 0.05). Although we did not evaluate the intestinal activities of MAO and DAO, our results suggest that healthy adult dogs have an efficient deamination process on the gut epithelium. [ABSTRACT FROM AUTHOR]

Periodic food shortage is a common ecological stressor for animals, likely to drive physiological and metabolic adaptations to alleviate its consequences, particularly for juveniles that have no option but to continue to grow and develop despite undernutrition. Here we study changes in metabolism associated with adaptation to nutrient shortage, evolved by replicate Drosophila melanogaster populations maintained on a nutrient-poor larval diet for over 240 generations. In a factorial metabolomics experiment we showed that both phenotypic plasticity and genetically-based adaptation to the poor diet involved wide-ranging changes in metabolite abundance; however, the plastic response did not predict the evolutionary change. Compared to nonadapted larvae exposed to the poor diet for the first time, the adapted larvae showed lower levels of multiple free amino acids in their tissues—and yet they grew faster. By quantifying accumulation of the nitrogen stable isotope 15N we show that adaptation to the poor diet led to an increased use of amino acids for energy generation. This apparent "waste" of scarce amino acids likely results from the trade-off between acquisition of dietary amino acids and carbohydrates observed in these populations. The three branched-chain amino acids (leucine, isoleucine, and valine) showed a unique pattern of depletion in adapted larvae raised on the poor diet. A diet supplementation experiment demonstrated that these amino acids are limiting for growth on the poor diet, suggesting that their low levels resulted from their expeditious use for protein synthesis. These results demonstrate that selection driven by nutrient shortage not only promotes improved acquisition of limiting nutrients, but also has wide-ranging effects on how the nutrients are used. They also show that the abundance of free amino acids in the tissues does not, in general, reflect the nutritional condition and growth potential of an animal. [ABSTRACT FROM AUTHOR]

5-Methyl-2'-deoxycytidine (mC) at CpG sites plays a key role in the epigenetic gene regulation, cell differentiation, and carcinogenesis. Despite the importance of mC for normal cell function, CpG dinucleotides are known as mutagenesis hotspots. Deamination of mC yields T, causing C→T transitions. However, several recent studies demonstrated the effect of epigenetic modifications of C on the fidelity and efficiency of DNA polymerases and excision repair enzymes. The review summarizes the available data that indicate the existence of deamination-independent mechanisms of mutagenesis at CpG sites. [ABSTRACT FROM AUTHOR]

Current DNA base editors contain nuclease and DNA deaminase that enables deamination of cytosine (C) or adenine (A), but no method for guanine (G) or thymine (T) editing is available at present. Here we developed a deaminase-free glycosylase-based guanine base editor (gGBE) with G editing ability, by fusing Cas9 nickase with engineered N-methylpurine DNA glycosylase protein (MPG). By several rounds of MPG mutagenesis via unbiased and rational screening using an intron-split EGFP reporter, we demonstrated that gGBE with engineered MPG could increase G editing efficiency by more than 1500 fold. Furthermore, this gGBE exhibited high base editing efficiency (up to 81.2%) and high G-to-T or G-to-C (i.e. G-to-Y) conversion ratio (up to 0.95) in both cultured human cells and mouse embryos. Thus, we have provided a proof-of-concept of a new base editing approach by endowing the engineered DNA glycosylase the capability to selectively excise a new type of substrate. [ABSTRACT FROM AUTHOR]

The mechanisms for the deamination reactions of 6-thioguanine (6-TG) with H2O, OH−, and OH−/H2O and for protonated 6-thioguanine (6-TGH+) with H2O have been studied by theoretical calculations. Six pathways, paths A–F, have been explored and relative energies, enthalpies, and Gibbs energies were calculated for each reaction path. Compared with the deamination reaction of 6-TG with H2O or 6-TGH+ with H2O, the deamination reaction of 6-TG with OH− shows a lower overall Gibbs energy of activation, indicating that the 6-TG deamination reaction is favorably to occur for the deprotonated form 6-TG− with H2O. With the assistance of an additional water molecule, the deamination reaction of 6-TG with OH−/H2O (path F) is found to be the most feasible pathway in gas phase and also in aqueous solution. The overall Gibbs energy of activation for path F in gas phase and in aqueous solution is 169.8 and 140.6 kJ mol−1 (SMD model), respectively, at the B3LYP/6–311++G(d,p) level of theory. [ABSTRACT FROM AUTHOR]

The RGD motif on the SARS-CoV-2 spike protein has been suggested to interact with RGD-binding integrins αVβ3 and α5β1 to enhance viral cell entry and alter downstream signaling cascades. The D405N mutation on the Omicron subvariant spike proteins, resulting in an RGN motif, has recently been shown to inhibit binding to integrin αVβ3. Deamidation of asparagines in protein ligand RGN motifs has been demonstrated to generate RGD and RGisoD motifs that permit binding to RGD-binding integrins. Two asparagines, N481 and N501, on the Wild-type spike receptor-binding domain have been previously shown to have deamidation half-lives of 16.5 and 123 days, respectively, which may occur during the viral life cycle. Deamidation of Omicron subvariant N405 may recover the ability to interact with RGD-binding integrins. Thus, herein, all-atom molecular dynamics simulations of the Wild-type and Omicron subvariant spike protein receptor-binding domains were conducted to investigate the potential for asparagines, the Omicron subvariant N405 in particular, to assume the optimized geometry for deamidation to occur. In summary, the Omicron subvariant N405 was primarily found to be stabilized in a state unfavourable for deamidation after hydrogen bonding with downstream E406. Nevertheless, a small number of RGD or RGisoD motifs on the Omicron subvariant spike proteins may restore the ability to interact with RGD-binding integrins. The simulations also provided structural clarification regarding the deamidation rates of Wild-type N481 and N501 and highlighted the utility of tertiary structure dynamics information in predicting asparagine deamidation. Further work is needed to characterize the effects of deamidation on spike-integrin interactions. • The deamidation mechanisms of Wild-type N481 and N501 were further elucidated. • Hydrogen bonding and backbone constraints interfere with Omicron N405 deamidation. • The Q498R mutation affects potential deamidation of distant asparagines. • Slow deamidation of N405 may result in a mixture of spike protein RGD/RGisoD motifs. [ABSTRACT FROM AUTHOR]

Adenosine-to-inosine tRNA-editing enzyme has been identified for more than two decades, but the study on its DNA editing activity is rather scarce. We show that amphioxus (Branchiostoma japonicum) ADAT2 (BjADAT2) contains the active site 'HxE-PCxxC' and the key residues for target-base-binding, and amphioxus ADAT3 (BjADAT3) harbors both the N-terminal positively charged region and the C-terminal pseudo-catalytic domain important for recognition of substrates. The sequencing of BjADAT2-transformed Escherichia coli genome suggests that BjADAT2 has the potential to target E. coli DNA and can deaminate at TCG and GAA sites in the E. coli genome. Biochemical analyses further demonstrate that BjADAT2, in complex with BjADAT3, can perform A-to-I editing of tRNA and convert C-to-U and A-to-I deamination of DNA. We also show that BjADAT2 preferentially deaminates adenosines and cytidines in the loop of DNA hairpin structures of substrates, and BjADAT3 also affects the type of DNA substrate targeted by BjADAT2. Finally, we find that C89, N113, C148 and Y156 play critical roles in the DNA editing activity of BjADAT2. Collectively, our study indicates that BjADAT2/3 is the sole naturally occurring deaminase with both tRNA and DNA editing capacity identified so far in Metazoa. An adenosine-to-inosine tRNA-editing deaminase ADAT2 from amphioxus (Branchiostoma japonicum) in complex with ADAT3 can perform A-to-I editing of tRNA and convert C-to-U and A-to-I deamination of DNA. [ABSTRACT FROM AUTHOR]