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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]

Objectives Methods Results Conclusions The hair shaft is often exposed to shampoo and haircare products that have unknown or varying pH levels. These products contain a combination of surfactants and other active ingredients to treat the hair or the scalp. As amphoteric proteins, hair keratins have limited buffering capacity, so variations in pH can have multifaceted impacts on them. However, there is limited knowledge about how pH affects keratins and keratin‐associated proteins (KAPs). Therefore, this study aims to examine the effects of varying pH levels (pH 3–pH 12) on hair structure and analyse consequent alterations in the hair proteome using mass spectrometry‐based proteomics.A scanning electron microscope was used to examine changes in hair‐shaft morphology due to exposure to various pH levels, while mass spectrometry was employed to analyse protein alterations.We found that exposing the hair shaft to varying pH levels led to specific effects on the cuticle, including cuticle lifting at certain pH levels, while proteomics analysis identified alterations in the hair proteome along with significant deamidation of keratins types I and II and KAPs. More pronounced effects were observed at extreme acidic conditions (pH 3) and alkaline conditions (above pH 8) on both hair morphology and hair proteins. pH levels between pH 5 and pH 7 had minimal impact on hair structure and proteins, suggesting that haircare products with pH in this range are ideal for hair‐shaft health. In contrast, alkaline pH levels were found to negatively affect hair.The structure evaluation and proteomics data emphasize the critical role of pH in hair health. The extreme acidic or alkaline pH impacts the hair structure and hair proteins. The study highlights the optimal pH range for maintaining healthy hair. [ABSTRACT FROM AUTHOR]

The lack of fat in yogurt can lead to alterations in taste and whey separation, reducing consumer acceptance. In this study, the feasibility of enhancing the quality of skim milk yogurt through a combination of transglutaminase (TG) and protein-glutaminase (PG) was investigated. The combination of TG and PG resulted in simultaneous cross-linking and deamidation of CN micelles, with PG deamidation taking priority over TG cross-linking, leading to higher solubility and lower turbidity of milk proteins compared with TG alone. When 0.06 U/mL TG and 0.03 U/mL PG were added, firmness and viscosity indexes significantly increased by 38.26% and 78.59%, respectively, as compared with the control. Microscopic images revealed increased cross-linking with CN and filling of cavities by smaller submicelles in the combination of TG and PG treatment. Furthermore, the combination of TG and PG resolved issues of rough taste and whey separation, leading to improved overall liking. This study highlights the benefits of using both enzymes in dairy production and has important implications for future research. The list of standard abbreviations for JDS is available at adsa.org/jds-abbreviations-24. Nonstandard abbreviations are available in the Notes. [Display omitted] [ABSTRACT FROM AUTHOR]

Various cis- and trans-aziridine derivatives were deaminated via the reaction with task-specific silica immobilized organosilane-based nitrite ionic liquid. Corresponding cis- or trans-alkenes were produced as stereospecific products in good-to-excellent yields. The advantages of this method include the one-pot procedure, operational simplicity, solvent-free, and very short reaction times. Simple handling of this nitrite anion source nanoparticles and thus lowering the risks and hazards of a chemical process can offer other important advantages. [ABSTRACT FROM AUTHOR]

The biocatalytic oxidative deamination‐ reductive amination process for the production of L‐phosphinothricin (L‐PPT) from D,L‐phosphinothricin (D,L‐PPT) is a green and environmentally friendly approach with significant development potential. In this study, the adopted technological route involves the oxidative deamination of the D‐PPT component in D,L‐PPT to 2‐oxo‐4‐(hydroxymethylphosphinyl)butanoic acid (PPO) by utilizing D‐amino acid oxidase (DAAO), followed by the catalytic reductive amination of PPO to L‐PPT using phosphinothricin dehydrogenase (PpDH). In order to enhance the catalytic rate and reduce the inhibitory effect of the intermediate product PPO on the catalytic process, optimization of both oxidative deamination and reductive amination phases was conducted through separate strategies of constant‐pressure oxygen supply and substrate feeding, respectively. A "two‐step one‐pot" method was employed to link the optimized reactions, significantly shortening the production time. Furthermore, the "two‐step one‐pot" catalytic strategy was optimized, ultimately achieving a high 97.7% yield of L‐PPT with ee of L‐PPT>99.9% after 5.5 h of reaction under 800 mM D,L‐PPT catalytic conditions, D‐PPT and PPO could not bedetected in the reaction system, further enchanced the catalytic efficiency, production efficiency and product quality. The aforementioned results demonstrate that this proposed approach has great potential for industrial‐scale production of L‐PPT as well as significant competitive advantages in terms of economic feasibility. [ABSTRACT FROM AUTHOR]

Creating cross‐linking to establish efficient inter‐chain charge‐transfer channels in carbon nitride represents a promising strategy for enhancing its photocatalytic capabilities. Molten salt‐assisted calcining has emerged as a method for preparing cross‐linked carbon nitrides. However, the precise influence of molten salts on the molecular structure of carbon nitride remains to be fully elucidated. Herein, we develop a KCl guided cross‐linking reaction to preliminarily reveal the formation mechanism of cross‐linking. The cross‐linking reaction is initiated by the pre‐coordination of amino groups with K+. Subsequent heating at high temperature converts the amino groups into chlorines. Then, dechlorination leads to the formation of cross‐linking. Thus, this cross‐linking reaction can be accurately described as a pre‐coordination‐induced, two‐step deamination reaction. The pre‐coordination step plays a pivotal role in the cross‐linking process. Sufficient pre‐coordination results in a relatively high cross‐linking degree of the as‐prepared CNK‐2. Consequently, CNK‐2 demonstrates a significantly enhanced photocatalytic H2O2 production, with a generation rate of 682 μmol L−1 h−1, about 59 times that of traditional carbon nitride. [ABSTRACT FROM AUTHOR]

Radical S‐adenosyl‐L‐methionine (SAM) enzymes couple the reductive cleavage of SAM to radical‐mediated transformations that have proven to be quite broad in scope. DesII is one such enzyme from the biosynthetic pathway of TDP‐desosamine where it catalyzes a radical‐mediated deamination. Previous studies have suggested that this reaction proceeds via direct elimination of ammonia from an α‐hydroxyalkyl radical or its conjugate base (i.e., a ketyl radical) rather than 1,2‐migration of the amino group to form a carbinolamine radical intermediate. However, without a crystal structure, the active site features responsible for this chemistry have remained largely unknown. The crystallographic studies described herein help to fill this gap by providing a structural description of the DesII active site. Computational analyses based on the solved crystal structure are consistent with direct elimination and indicate that an active site glutamate residue likely serves as a general base to promote deprotonation of the α‐hydroxyalkyl radical intermediate and elimination of the ammonia group. [ABSTRACT FROM AUTHOR]

The jet impingement–negative‐pressure reactor (JI‐NPR) is a continuous and efficient technology designed to remove ammonia without clogging. Prior research has discovered that the changing movement of a porous jet impinging under negative‐pressure conditions is distinguished by a more pronounced distribution over many regions. This study utilizes the CFD numerical simulation method in conjunction with the MATLAB platform to investigate the fractal characteristics of water phase distribution, velocity, turbulence intensity, vortex amount, and other parameters at various locations. The fractal dimension is employed as a criterion to analyze the chaotic characteristics of this multi‐area distribution phenomenon. The study demonstrates that the effectiveness of deamination removal can be enhanced by quantitatively assessing the complex characteristics in the fluid flow using the chaotic fractal theory, which facilitates the identification of the ideal parameter settings. The optimal deamination effect can be achieved in the reactor when the jet velocity is set to 3.45 m/s and the negative pressure is maintained at 20 400 Pa. [ABSTRACT FROM AUTHOR]

Elemental sulfur has shown to be a promising alternative feedstock for development of novel polymeric materials with high sulfur content. However, the utilization of inverse vulcanized polymers is restricted by the limitation of functional comonomers suitable for an inverse vulcanization. Control over properties and structure of inverse vulcanized polymers still poses a challenge to current research due to the dynamic nature of sulfur‐sulfur bonds and high temperature of inverse vulcanization reactions. In here, we report for the first time the inverse vulcanization of norbornenyl pentafluorophenyl ester (NB‐PFPE), allowing for post‐modification of inverse vulcanized polymers via amidation of reactive PFP esters to yield high sulfur content polymers under mild conditions. Amidation of the precursor material with three functional primary amines (α‐amino‐ω‐methoxy polyethylene glycol, aminopropyl trimethoxy silane, allylamine) was investigated. The resulting materials were applicable as sulfur containing poly(ethylene glycol) nanoparticles in aqueous environment. Cross‐linked mercury adsorbents, sulfur surface coatings, and high‐sulfur content networks with predictable thermal properties were achievable using aminopropyl trimethoxy silane and allylamine for post‐polymerization modification, respectively. With the broad range of different amines available and applicable for post‐polymerization modification, the versatility of poly(sulfur‐random‐NB‐PFPE) as a platform precursor polymer for novel specialized sulfur containing materials was showcased. [ABSTRACT FROM AUTHOR]

The article discusses the polymerization scheme of benzoxazine monomer based on 4,4′‐diaminodiphenylmethane (P‐ddm) and the chemical structure of polybenzoxazine based on it poly(P‐ddm). The polymerization behavior of benzoxazine P‐ddm is studied using differential scanning calorimetry (DSC). Solid‐state 13C MAS NMR is used to determine the chemical structure of poly(P‐ddm). It is revealed that the сhemical structure of poly(P‐ddm) predominantly consists not of phenolic Mannich bridges, as expected, but of methylene bridges, which indicates the process of deamination of phenolic Mannich bridges. However, no weight loss associated with the expected release of free amine during this process is detected. This may indicate the incorporation of a diamine moiety into the polymer chain through the formation of imine bonds, the signal of which is detected in the 13C MAS NMR and FTIR spectra of the poly(P‐ddm), and on the 1H and 13C NMR spectra of model polybenzoxazine based on p‐cresol and 4,4′‐diaminodiphenylmethane poly(pC‐ddm). Based on the data obtained, a hypothesis is put forward about the formation of a network polymer, the structure of which consists mainly of methylene and imine units. [ABSTRACT FROM AUTHOR]

Therapeutic antibodies such as monoclonal antibodies (mAbs), bispecific and multispecific antibodies are pivotal in therapeutic protein development and have transformed disease treatments across various therapeutic areas. The integrity of therapeutic antibodies, however, is compromised by sequence liabilities, notably deamidation, where asparagine (N) and glutamine (Q) residues undergo chemical degradations. Deamidation negatively impacts the efficacy, stability, and safety of diverse classes of antibodies, thus necessitating the critical need for the early and accurate identification of vulnerable sites. In this article, a comprehensive antibody deamidation-specific dataset (n = 2285) of varied modalities was created by using high-throughput automated peptide mapping followed by supervised machine learning to predict the deamidation propensities, as well as the extents, throughout the entire antibody sequences. We propose a novel chimeric deep learning model, integrating protein language model (pLM)-derived embeddings with local sequence information for enhanced deamidation predictions. Remarkably, this model requires only sequence inputs, eliminating the need for laborious feature engineering. Our approach demonstrates state-of-the-art performance, offering a streamlined workflow for high-throughput automated peptide mapping and deamidation prediction, with the potential of broader applicability to other antibody sequence liabilities. [ABSTRACT FROM AUTHOR]

The viral infectivity factor (Vif) of human immunodeficiency virus 1 forms a complex with host proteins, designated as Vif-CBFβ-ELOB-ELOC-CUL5 (VβBCC), initiating the ubiquitination and subsequent proteasomal degradation of the human antiviral protein APOBEC3G (A3G), thereby negating its antiviral function. Whilst recent cryo-electron microscopy (cryo-EM) studies have implicated RNA molecules in the Vif-A3G interaction that leads to A3G ubiquitination, our findings indicated that the VβBCC complex can also directly impede A3G-mediated DNA deamination, bypassing the proteasomal degradation pathway. Employing the Systematic Evolution of Ligands by EXponential enrichment (SELEX) method, we have identified RNA aptamers with high affinity for the VβBCC complex. These aptamers not only bind to the VβBCC complex but also reinstate A3G's DNA deamination activity by inhibiting the complex's function. Moreover, we delineated the sequences and secondary structures of these aptamers, providing insights into the mechanistic aspects of A3G inhibition by the VβBCC complex. Analysis using selected aptamers will enhance our understanding of the inhibition of A3G by the VβBCC complex, offering potential avenues for therapeutic intervention. [ABSTRACT FROM AUTHOR]

An efficient approach to the synthesis of novel 2,3-diaryl-3,4-dihydro-2H-benzo[4,5]imidazo[2,1-b][1,3,4]thiadiazines via a base-catalyzed intramolecular cyclization of 2-arylmethylthio-N-arylidene-1H-benzo[d]imidazol-1-amines has been developed. The use of alkali is critical for the annulation of the thiadiazine ring. In the absence of strong bases, the starting compounds undergo deamination with elimination of benzonitrile and formation of 2-arylmethylthiobenzimidazoles. [ABSTRACT FROM AUTHOR]

Abstract Deamination of bases is a form of DNA damage that occurs spontaneously via the hydrolysis and nitrosation of living cells, generating hypoxanthine from adenine. E. coli endonuclease V (eEndoV) cleaves hypoxanthine-containing double-stranded DNA, whereas human endonuclease V (hEndoV) cleaves hypoxanthine-containing RNA; however, hEndoV in vivo function remains unclear. To date, hEndoV has only been examined using hypoxanthine, because it binds closely to the base located at the cleavage site. Here, we examined whether hEndoV cleaves other lesions (e.g., AP site, 6-methyladenine, xanthine) to reveal its function and whether 2′-nucleoside modification affects its cleavage activity. We observed that hEndoV is hypoxanthine-specific; its activity was the highest with 2′-OH modification in ribose. The cleavage activity of hEndoV was compared based on its base sequence. We observed that it has specificity for adenine located on the 3′-end of hypoxanthine at the cleavage site, both before and after cleavage. These data suggest that hEndoV recognizes and cleaves the inosine generated on the poly A tail to maintain RNA quality. Our results provide mechanistic insight into the role of hEndoV in vivo.

l-glutamate is an umami component found in various foods, and l-glutamate oxidase (LGOX, EC 1.4.3.11) is a FAD-dependent oxidoreductase that catalyzes the oxidative deamination of l-glutamate. A recently reported single-chain LGOX mutant from Streptomyces sp. X-119-6 is a potential material for l-glutamate sensors because this mutant is easier to prepare than the wild type. Herein, we report the development of a simple analytical kit using this LGOX mutant for the on-site quantification of l-glutamate. The kit named PACKTEST was developed using a colorimetric method to estimate the l-glutamate concentration in the range of 1–50 mg/L through the visual comparison of the resulting sample color with a standard color sequence. In addition, the PACKTEST kit was combined with a portable photometer for the spectrophotometric quantification of l-glutamate in the range of 0.5–12.0 mg/L. It was used to quantify l-glutamate in commercially available soy sauces, and the results were in good agreement (r = 0.97) with the values obtained by post-column derivatized ion-exchange chromatography. Furthermore, we loaded and dried all the reagents, including enzymes, on a 96- well plate to prepare an enzyme-based sensing device, which showed potential for the high-throughput quantification of l-glutamate. [ABSTRACT FROM AUTHOR]

A hydrophobic Ni‐PTFE modified electrode has been prepared by constant current and cathodic electroplating with a nickel sheet as substrate in a PTFE suspension. Then the Ni‐PTFE modified electrode was used for electroreduction from aromatic amide to diarylimide. The electrochemical characterizations such as cyclic voltammogram, EIS, polarization curves, and electrode stability have been carried out by electrochemical workstation. The structure of the electroreduction product diarylimide was characterized by 1H NMR, FT‐IR, MS(Mass Spectrum), and EA(Elemental Analyzer). Based on the hydrophobicity of the electrode, an approach suggested that the phenyl ketone radical may be formed by electroreductive deamination at the cathode. With the construction of C−N bond by the radical coupling, the electrocatalytic reduction may be comprised of a one‐electron process including an ECC (Electrochemical‐Chemical‐Chemical) process. The electroreduction of aromatic amide to diarylimide may be controlled by both charge migration and concentration polarization. Electrocatalytic reduction of aromatic amides on Ni‐PTFE modified electrodes is all well conversion ratio. [ABSTRACT FROM AUTHOR]

The development of an efficient alternative to the widely employed Balz‐Schiemann deaminative fluorination method (i. e. without using aryl diazonium tetrafluoroborate salt) is a challenging task. Herein, we report a convenient one‐pot method for the FeCl3‐nanocellullose mediated mechanochemical synthesis of fluoroarenes through the selective substitution of an aromatic amino group by fluorine group using pyrylium tetrafluoroborate (Pyry‐BF4) and sodium fluoride (NaF) via in situ formation of pyridinium salt intermediate. The scope of the present protocol includes synthesis of thirty‐four organofluorine compounds with excellent yields via a selective substitution (SNAr) of an amino group by fluorine. The presented concise methodology opens a pathway to access new chemical spaces for the late‐stage functionalization in pharmaceutical industries. [ABSTRACT FROM AUTHOR]

• A comprehensive forced stress study involving different sources of stress and analysis by various analytical and characterization techniques elucidates the product stability, degradation products, and pathways of asymmetric monovalent bispecific IgG1 monoclonal antibody produced using duet mAb technology, which to our knowledge has not been reported so far. • The duet mAb exhibits structural integrity, degradation products, and overall stability identical to a standard IgG1 mAb. • The study demonstrates the prominent stability of an asymmetric bispecific IgG1 mAb format as a stable biotherapeutic platform. The developed asymmetric monovalent bispecific IgG1 or Duet monoclonal antibody (Duet mAb) has two distinct fragment antigen-binding region (Fab) subunits that target two different epitope specificities sequentially or simultaneously. The design features include unique engineered disulfide bridges, knob-into-hole mutations, and kappa and lambda chains to produce Duet mAbs. These make it structurally and functionally complex, so one expects challenging developability linked to instability, degradation of products and pathways, and limited reports available. Here, we have treated the product with different sources of extreme stress over a lengthy period, including varying heat, pH, photo stress, chemical oxidative stress, accelerated stress in physiological conditions, and forced glycation conditions. The effects of different stress conditions on the product were assessed using various analytical characterization tools to measure product-related substances, post-translational modifications (PTMs), structural integrity, higher-order disulfide linkages, and biological activity. The results revealed degradation products and pathways of Duet mAb. A moderate increase in size, charge, and hydrophobic variants, PTMs, including deamidation, oxidation, isomerization, and glycation were observed, with most conditions exhibiting biological activity. In addition, the characterization of fractionated charge variants, including deamidated species, showed satisfactory biological activity. This study demonstrated the prominent stability of the Duet mAb format comparable to most marketed mAbs. [ABSTRACT FROM AUTHOR]

The electrochemical advanced oxidation process (EAOP) has shown significant promise in the field of refractory organic wastewater treatment due to its high efficiency and environmentally friendly nature. In this study, Ti/Sb-SnO2 electrodes with varying proportions of Hf were prepared using the sol–gel method. The addition of Hf transformed the original collapsing and broken surface into a flat and regular surface. The results demonstrated that Ti/Sb-SnO2-Hf electrode doped with 6% Hf exhibited a higher oxygen evolution potential (OEP) and excellent stability. The OEP increased from 2.315 V without Hf-doping to 2.482 V, and the corresponding actual life was 321.05% higher than that without Hf. The current density (5–40 mA·cm−2), electrolyte concentration (0.02–0.2 mol·L−1), pH (3–11), and initial pollutant concentration (5–80 mg·L−1) were evaluated to confirm the tetracycline (TC) degradation characterization of Ti/Sb-SnO2-6%Hf electrodes. It was concluded that under the optimal degradation conditions, the removal rate of TC could reach 99.66% within 2 h. The degradation of TC follows first-order reaction kinetics. The oxidative degradation of TC was achieved through indirect oxidation, with ·OH playing a dominant role. TC's electrochemical oxidation degradation pathway has been proposed: Based on LC–MS results, three main pathways are speculated. During the electrocatalytic oxidation process, decarboxylation, deamidation, and ring-opening reactions occur under ·OH attack, producing intermediate compounds with m/z values of 427, 433, 350, 246, 461, 424, 330, 352, 309, 263, and 233. These intermediates are further oxidized to intermediate compounds with an m/z value of 218. This work introduces a new efficient anode electrochemical catalyst for the degradation of TC, providing a strategy for industrial applications. [ABSTRACT FROM AUTHOR]

Site-specific modifications of aspartate residues spontaneously occur in crystallin, the major protein in the lens. One of the primary modification sites is Asp151 in αA-crystallin. Isomerization and racemization alter the crystallin backbone structure, reducing its stability by inducing abnormal crystallin–crystallin interactions and ultimately leading to the insolubilization of crystallin complexes. These changes are considered significant factors in the formation of senile cataracts. However, the mechanisms driving spontaneous isomerization and racemization have not been experimentally demonstrated. In this study, we generated αA-crystallins with different homo-oligomeric sizes and/or containing an asparagine residue at position 151, which is more prone to isomerization and racemization. We characterized their structure, hydrophobicity, chaperone-like function, and heat stability, and examined their propensity for isomerization and racemization. The results show that the two differently sized αA-crystallin variants possessed similar secondary structures but exhibited different chaperone-like functions depending on their oligomeric sizes. The rate of isomerization and racemization of Asp151, as assessed by the deamidation of Asn151, was also found to depend on the oligomeric sizes of αA-crystallin. The predominant isomerization product via deamidation of Asn151 in the different-sized αA-crystallin variants was L-β-Asp in vitro, while various modifications occurred around Asp151 in vivo. The disparity between the findings of this in vitro study and in vivo studies suggests that the isomerization of Asp151 in vivo may be more complex than what occurs in vitro. [ABSTRACT FROM AUTHOR]

Mammalian transglutaminases, a family of Ca2+-dependent proteins, are implicated in a variety of diseases. For example, celiac disease (CeD) is an autoimmune disorder whose pathogenesis requires transglutaminase 2 (TG2) to deamidate select glutamine residues in diet-derived gluten peptides. Deamidation involves the formation of transient γ-glutamyl thioester intermediates. Recent studies have revealed that in addition to the deamidated gluten peptides themselves, their corresponding thioester intermediates are also pathogenically relevant. A mechanistic understanding of this relevance is hindered by the absence of any structure of Ca2+-bound TG2. We report the X-ray crystallographic structure of human TG2 bound to an inhibitory gluten peptidomimetic and two Ca2+ ions in sites previously designated as S1 and S3. Together with additional structure-guided experiments, this structure provides a mechanistic explanation for how S1 regulates formation of an inhibitory disulfide bond in TG2, while also establishing that S3 is essential for γ-glutamyl thioester formation. Furthermore, our crystallographic findings and associated analyses have revealed that i) two interacting residues, H305 and E363, play a critical role in resolving the thioester intermediate into an isopeptide bond (transamidation) but not in thioester hydrolysis (deamidation); and ii) residues N333 and K176 stabilize preferred TG2 substrates and inhibitors via hydrogen bonding to nonreactive backbone atoms. Overall, the intermediate-state conformer of TG2 reported here represents a superior model to previously characterized conformers for both transition states of the TG2-catalyzed reaction. [ABSTRACT FROM AUTHOR]

Motivation The alignment of sequencing reads is a critical step in the characterization of ancient genomes. However, reference bias and spurious mappings pose a significant challenge, particularly as cutting-edge wet lab methods generate datasets that push the boundaries of alignment tools. Reference bias occurs when reference alleles are favoured over alternative alleles during mapping, whereas spurious mappings stem from either contamination or when endogenous reads fail to align to their correct position. Previous work has shown that these phenomena are correlated with read length but a more thorough investigation of reference bias and spurious mappings for ancient DNA has been lacking. Here, we use a range of empirical and simulated palaeogenomic datasets to investigate the impacts of mapping tools, quality thresholds, and reference genome on mismatch rates across read lengths. Results For these analyses, we introduce AMBER, a new bioinformatics tool for assessing the quality of ancient DNA mapping directly from BAM-files and informing on reference bias, read length cut-offs and reference selection. AMBER rapidly and simultaneously computes the sequence read mapping bias in the form of the mismatch rates per read length, cytosine deamination profiles at both CpG and non-CpG sites, fragment length distributions, and genomic breadth and depth of coverage. Using AMBER, we find that mapping algorithms and quality threshold choices dictate reference bias and rates of spurious alignment at different read lengths in a predictable manner, suggesting that optimized mapping parameters for each read length will be a key step in alleviating reference bias and spurious mappings. Availability and implementation AMBER is available for noncommercial use on GitHub (https://github.com/tvandervalk/AMBER.git). Scripts used to generate and analyse simulated datasets are available on Github (https://github.com/sdolenz/refbias_scripts). [ABSTRACT FROM AUTHOR]

Deamidation is a post-translational chemical modification that occurs within proteins and can be influenced by many factors, including temperature and pH. In vaccines, deamidation is considered undesirable as it may lead to changes in structure, function, stability, and immunogenicity. Detecting deamidation in vaccines, especially adjuvanted vaccines, can be challenging due to the lack of simple quantitative techniques. In this study, the quantification of isoaspartic acid (isoAsp) was used to assess deamidation in model antigens in the presence and absence of common vaccine adjuvants. This study shows that the detection of isoAsp was possible in the presence of various types of adjuvants with little to no interference. High levels of isoAsp were detected in thermally and pH-stressed adjuvanted vaccines, suggesting significant deamidation and highlighting the stability-indicating capabilities of the assay. The quantification of isoAsp in stability programs of a vaccine drug product could possibly find applications in product shelf-life determination, using thermal kinetic modeling to predict deamidation over time. The ability to detect deamidation early in vaccine development enhances process improvements and ultimately improves the vaccine's stability. To summarize, this paper describes a rapid and simple method to determine deamidation in adjuvanted vaccines. This method could be applicable to formulation development, stability assessment, or shelf-life determination. [ABSTRACT FROM AUTHOR]

Herein, we disclose that pyridinium salts derived from abundant (hetero)anilines represent a novel precursor class for nucleophilic aromatic substitution reactions with [18F]fluoride. The value of this new 18F‐fluorodeamination is demonstrated with the synthesis of over 30 structurally diverse and complex heteroaryl 18F‐fluorides, several derived from scaffolds that were yet to be labelled with fluorine‐18. The protocol tolerates heteroarenes and functionalities commonly found in drug discovery libraries, and is amenable to scale‐up and automation on a commercial radiosynthesiser. [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]

In this study, chitosan-based surfactants were synthesized by epoxy–amine chemistry to stabilize concentrated O/W emulsions at pH7. Chitosan was first depolymerized by nitrous deamination to obtain chitooligosaccharides (COS) with degrees of polymerization of 10 (DP10) and 20 (DP20). Then, three different epoxidized fatty chains, i.e., octyl/decyl glycidyl ether (C9), hexadecyl glycidyl ether (C16) and epoxidized cardanol (card), were grafted onto the amine groups of chitosan to form six amphiphilic structures. NMR measurements revealed grafting efficiencies ranging from 1 to 30% while HLB values ranged from 13 to 20. The relationships between these surfactant structures and their adsorption properties were investigated by tensiometric measurements, highlighting the need for a short hydrophilic moiety and high grafting efficiency to obtain the best adsorption. Subsequently, concentrated O/W emulsions (66% of oil) at pH7 were produced using COS-based surfactants and the impact of stirring time and speed during the emulsification process was described through rheological, droplet size and microscopy measurements. Finally, emulsions were stored over 2 months in order to study the destabilization phenomenon into the mixture, i.e., coalescence and creaming, by using laser granulometry and Turbiscan. Results demonstrated that stability could be enhanced by increasing emulsion viscosity, reducing droplet size or optimizing the adsorption layer at the O/W interfaces. [ABSTRACT FROM AUTHOR]

The obligate intracellular bacterium, Chlamydia trachomatis, has evolved to depend on its human host for many metabolites, including most amino acids and three of the four nucleotides. Given this, it is not surprising that depletion of a single amino acid in the host cell growth medium blocks chlamydial replication. Paradoxically, supra-normal levels of some amino acids also block productive replication of Chlamydia. Here, we have determined how elevated serine levels, generated by exogenous supplementation, impede chlamydial inclusion development and reduce the generation of infectious progeny. Our findings reveal that human serine racemase, which is broadly expressed in multiple tissues, potentiates the anti-chlamydial effect of elevated serine concentrations. In addition to reversibly converting l-serine to d-serine, serine racemase also deaminates serine via β-elimination. We have determined that d-serine does not directly impact Chlamydia; rather, ammonia generated by serine deamination limits the productive chlamydial replication. Our findings imply that ammonia produced within host cells can traverse the chlamydial inclusion membrane. Further, this property of serine deaminase can be exploited to sensitize Chlamydia to concentrations of doxycycline that are otherwise not bactericidal. Because exogenously elevated levels of serine can be tolerated over extended periods, the broad expression pattern of serine racemase indicates it to be a host enzyme whose activity can be directed against multiple intracellular bacterial pathogens. From a therapeutic perspective, demonstrating host metabolism can be skewed to generate an anti-bacterial metabolite that synergizes with antibiotics, we believe our results provide a new approach to target intracellular pathogens. [ABSTRACT FROM AUTHOR]

Over the past decade, the connection between APOBEC3 cytosine deaminases and cancer mutagenesis has become increasingly apparent. This growing awareness has created a need for biochemical tools that can be used to identify and characterize potential inhibitors of this enzyme family. In response to this challenge, we have developed a Real-time APOBEC3-mediated DNA Deamination assay. This assay offers a single-step set-up and real-time fluorescent read-out, and it is capable of providing insights into enzyme kinetics. The assay also offers a high-sensitivity and easily scalable method for identifying APOBEC3 inhibitors. This assay serves as a crucial addition to the existing APOBEC3 biochemical and cellular toolkit and possesses the versatility to be readily adapted into a high-throughput format for inhibitor discovery. [ABSTRACT FROM AUTHOR]

To alleviate amino acid imbalances in fermented soybean meal as a replacement for fishmeal feeds, this study evaluated the effects of adding lysine (Lys), methionine (Met), and α-ketoglutaric acid (AKG) to fermented soybean meals for Chinese perch. Chinese perch (34 ± 3 g) were fed five diets for 66 days (fishmeal as the protein source of the basal diet [FM]; fermented soybean meal as a substitute for 30% fishmeal in the soybean meal diet [FSM]; addition of crystalline Lys and Met [AA]; addition of α-ketoglutaric acid [AKG]; and simultaneous addition of crystalline Lys, Met, and AKG [BA] to the soybean meal diet). At the end of the feeding trial, the FSM group had the highest feeding rate and the lowest weight gain rate among all the groups. The FM group had the highest protein retention and the lowest feed efficiency among the groups. The mRNA transcription level of genes related to the AMP-activating protein (AMPK) signaling pathway and amino acid response (AAR) signaling pathway (lkb1, atf4, and gcn2) were highest in the AA group (P < 0.05) but lower in the AKG and BA groups. In the AKG group, the mRNA transcription level of the gluconeogenesis pathway-related gene (pepck and g6pase) was significantly higher than that in the other four groups, but the mRNA transcription level of genes related to amino acid catabolism (gdh and ampd) was lower. Among all the groups, the FSM group had the lowest mRNA transcription level of genes associated with the mammalian target of rapamycin (mTOR) signaling pathway (mtor and s6k). These findings imply that the feeding rate of Chinese perch in the fermented soybean meal group was the highest, but the protein retention was the lowest, while the addition of Lys, Met, and AKG improved protein retention. In conclusion, the addition of AKG to fermented soybean meal as a fishmeal substitute reduced amino acid deamination, enhanced gluconeogenesis, and increased protein deposition, which contributed to the growth of Chinese perch, alleviated amino acid imbalances, and improved the feed utilization of Chinese perch. [ABSTRACT FROM AUTHOR]

This review aims to highlight the structures of ADAR proteins that have been crucial in the discernment of their functions and are relevant to future therapeutic development. ADAR proteins can correct or diversify genetic information, underscoring their pivotal contribution to protein diversity and the sophistication of neuronal networks. ADAR proteins have numerous functions in RNA editing independent roles and through the mechanisms of A-I RNA editing that continue to be revealed. Provided is a detailed examination of the ADAR family members—ADAR1, ADAR2, and ADAR3—each characterized by distinct isoforms that offer both structural diversity and functional variability, significantly affecting RNA editing mechanisms and exhibiting tissue-specific regulatory patterns, highlighting their shared features, such as double-stranded RNA binding domains (dsRBD) and a catalytic deaminase domain (CDD). Moreover, it explores ADARs’ extensive roles in immunity, RNA interference, and disease modulation, demonstrating their ambivalent nature in both the advancement and inhibition of diseases. Through this comprehensive analysis, the review seeks to underline the potential of targeting ADAR proteins in therapeutic strategies, urging continued investigation into their biological mechanisms and health implications.

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]

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]

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]

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]

The formation of a rigid, tough interface based on a nacre-like structure in carbon fiber (CF) composites is a promising way to eliminate low delamination resistance. An effective method of coating CFs is electrophoretic deposition (EPD), which, in the case of dissimilar components like graphene oxide (GO) and polymeric glue, usually requires chemical bonding/strong interactions. In this work, we focus on chitin nanocrystals (ChNCs), leading to an excellent mechanical performance of artificial nacre, where favorable interactions and bonding with GO are controlled by degrees of deacetylation (5, 15, and 30%). We prepared coatings based on GO/ChNC adducts with 95/5, 90/10, 50/50, and 25/75 ratios using optimized EPD conditions (pH, concentration, voltage, and time). The prepared materials were characterized using FTIR, TEM, XPS, SEM, DLS, and XRD. SEM evaluation indicates the formation of a homogeneous interlayer, which has a fair potential for chemical bonding with the epoxy matrix. Short-beam testing of epoxy matrix composites indicates that the coating does not decrease stiffness and has a relatively low dependence on composition. Therefore, all coatings are promising for a detailed study of delamination resistance using laminate samples. Moreover, facile EPD from the water solution/suspension has a fair potential for industrial applications. [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]

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]

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]

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]

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]

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]