Unnatural Amino Acids for Biological Spectroscopy and Microscopy.

Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.

Visible-light-induced C(sp3)-H bromination of 4-methylthiophene derivatives with HBr/H2O2.

A convenient method to synthesize ethyl 4-(bromomethyl)thiophene-3-carboxylate derivatives has been developed via a visible-light-induced radical process in good yields and with wide functional group tolerance under air conditions and at ambient temperature. The present protocol has the advantages of a high atom economy, easy purification, and environmental friendliness as it employs HBr as the bromine source and the cheap and low-toxic H2O2 as the oxidant. The synthetic utility of this method is demonstrated by a gram scale reaction and its application in the innovative synthesis of the clinical drug relugolix.

Transport and fate of antibiotics in a typical aqua-agricultural catchment explained by rainfall events: Implications for catchment management.

Antibiotics receive many concerns since their negative environmental impacts are being revealed, especially in aqua-agricultural areas. Rainfall events are responsible for transferring excess contaminants to receiving waters. However, the understanding of antibiotics transport and fate responding to rainfall events was constrained by limited event-based data and lacking integrated consideration of dissolved and particulate forms. We developed an intensive monitoring strategy to capture responses of fourteen antibiotics to different types of rainfall events and inter-event low flow periods. Pollutant-rich suspended particles, as high as 1471 ng/g, were found in low flow periods while the very heavy rainfall events and consecutive rainfall events stimulated the release of antibiotics from eroded soil particles to river water. Therefore, these rainfall events drove radical increase of dissolved antibiotic concentration up to 592 ng/L and total flux up to 25.0 g/d. Sulfonamides were particularly sensitive to rainfall events because of their residues in manure-applied agricultural lands. Transport dynamics of most antibiotics were accretion whereas only clarithromycin exhibited a dilution pattern by concentration-discharge relationships. Aquaculture ponds were inferred to significantly contribute tetracycline, oxytetracycline, and clarithromycin. Conventional contaminants were compared to discriminate potential sources of antibiotics and imply effective catchment management. The results provided novel insights into event-based drivers and dynamics of antibiotics and could lead to appropriate management strategy.

C-H Imidation and Dual C-H Bond Aminobromination of Five-Membered Heterocycles.

Here, we report a practical C-H imidation of five-membered heterocycles under metal-free conditions. We also report the first dual C-H bond aminobromination of thiophenes, with benzotriazole, saccharin, 1,2,4-triazole, benzimidazole, pyrazole, 4-bromopyrazole, 5-methyltetrazole, and dibenzenesulfonimides as effective amine sources. Mechanistic studies support the radical pathway of the imidation and aminobromination reactions.

Characterization and source identification of tetracycline antibiotics in the drinking water sources of the lower Yangtze River.

The occurrence and spatio-temporal patterns of five tetracyclines (TCs) and six of their degradation products were investigated in twenty-eight drinking water sources along the lower Yangtze River (LYR) over dry, normal and flood seasons. Tetracycline (TC), oxytetracycline (OTC) and doxytetracycline (DXC) were the dominant antibiotics detected with the highest occurrence. The maximum concentrations of TC, OTC and DXC were found in dry season as 11.16, 18.98, and 56.09 ng/L, respectively, because of the low dilution, low degradation, and high consumption in this season. Cluster analysis indicated distinct variations in the TCs' compositional profiles in both space and time. OTC and its metabolites contributed 18.5-59.6% of the TC load in dry season, possibly due to the seasonally increased release of pharmaceutical OTCs from sewage effluents, but they were seldom detected in other seasons. Pollution load index analysis showed that tributaries carrying large amounts of veterinary TCs derived from breeding wastewater and untreated rural sewage contributed larger proportions of the TC load for most drinking water sources than sewage outlets. The contribution ratio of the TC load from tributaries (74.5%) was approximately three times higher than that from sewage discharges (25.5%). The study demonstrated that the control of load from tributaries is the key to mitigating TC pollution of the drinking water sources in the LYR. An effective source tracking method for evaluating the contribution of antibiotic load from multiple diffuse pollution origins and identifying the high-risk contamination sources was established for antibiotic management and control.

Copper-catalyzed C-N bond formation with imidazo[1,2-a]pyridines.

An efficient Cu-catalyzed method for direct C-N bond formation on the C-3 position of imidazo[1,2-a]pyridines is reported. The robust copper catalyst tolerated a wide range of functional groups and set the stage for the synthesis of diversely decorated imidazo[1,2-a]pyridines. Preliminary experimental results show that the reaction mechanism is consistent with C-3 radical functionalization.

Reorientation of the "free OH" group in the top-most layer of air/water interface of sodium fluoride aqueous solution probed with sum-frequency generation vibrational spectroscopy.

Many experimental and theoretical studies have established the specific anion, as well as cation, effects on the hydrogen-bond structures at the air/water interface of electrolyte solutions. However, the ion effects on the top-most layer of the air/water interface, which is signified by the non-hydrogen-bonded so-called "free OH" group, have not been explicitly discussed or studied. In this report, we present the measurement of changes of the orientational angle of the "free OH" group at the air/water interface of the sodium fluoride (NaF) solutions at different concentrations using the interface selective sum-frequency generation vibrational spectroscopy (SFG-VS) in the ssp and ppp polarizations. The polarization dependent SFG-VS results show that the average tilt angle of the "free OH" changes from about 36.6° ± 0.5° to 44.1° ± 0.6° as the NaF concentration increases from 0 to 0.94 M (nearly saturated). Such tilt angle change is around the axis of the other O-H group of the same water molecule at the top-most layer at the air/water interface that is hydrogen-bonded to the water molecules below the top-most layer. These results provide quantitative molecular details of the ion effects of the NaF salt on the structure of the water molecules at the top-most layer of the air/water interface, even though both the Na(+) cation and the F(-) anion are believed to be among the most excluded ions from the air/water interface.

Triple-Bond Vibrations: Emerging Applications in Energy and Biological Sciences.

Triple bonds, such as that formed between two carbon atoms (i.e., C≡C) or that formed between one carbon atom and one nitrogen atom (i.e., C≡N), afford unique chemical bonding and hence vibrational characteristics. As such, they are not only frequently used to construct molecules with tailored chemical and/or physical properties but also employed as vibrational probes to provide site-specific chemical and/or physical information at the molecular level. Herein, we offer our perspective on the emerging applications of various triple-bond vibrations in energy and biological sciences with a focus on C≡C and C≡N triple bonds.

Influence of potassium addition on phosphorus availability and heavy metals immobility of biochar derived from swine manure.

Pyrolysis of animal manure at high temperature is necessary to effectively immobilize heavy metals, while the available phosphorus (P) level in biochar is relatively low, rendering it unsuitable for use as fertilizer. In this study, the pretreatment of swine manure with different potassium (K) sources (KOH, K2CO3, CH3COOK and C6H5K3O7) was conducted to produce a biochar with enhanced P availability and heavy metals immobility. The addition of all K compounds lowered the peak temperature of decomposition of cellulose in swine manure. The percentage of ammonium citrate and formic acid extractable P in biochar increased with K addition compared to undoped biochar, with CH3COOK and C6H5K3O7 showing greater effectiveness than KOH and K2CO3, however, water- extractable P did not exhibit significant changes. Additionally, the available and dissolved Si increased due to the doping of K, with KOH and K2CO3 having a stronger effect than CH3COOK and C6H5K3O7. X-Ray Diffraction (XRD) and Fourier Transform Infrared Spectroscopy (FTIR) analysis revealed that K addition led to the formation of soluble CaKPO4 and silicate. In addition, the incorporation of K promoted the transformation of labile copper (Cu) and znic (Zn) into the stable fraction while simultaneously reducing their environmental risk. Our study suggest that the co-pyrolysis of swine manure and organic K represents an effective and valuable method for producing biochar with optimized P availability and heavy metals immobility.

Layer-specific mechanisms of perfluoroalkyl acid (PFAA) transport and partition in estuarine environments: Unveiling the depth-dependent differences.

Understanding of characteristics and transport of perfluoroalkyl acids (PFAAs) in heterogeneous estuarine environments is limited. Furthermore, the role of suspended particles (SPS) in different layers remains unclear. This study explores the multiphase distribution process and mechanism of PFAAs controlled by SPS across surface and bottom layers in five small estuaries. Peaks in PFAA concentrations are consistently observed at strongly stratified sites. Concentrations of the PFAAs in both surface and bottom SPS decreased as the degree of mixing increased from strongly stratified levels to well-mixed levels. The water-SPS partitioning of some short-chain PFAAs (PFBS, PFHxA, and PFHpA) is influenced by environmental factors (pH, depth, temperature, and salinity) due to electrostatic interactions, while the sorption of some long-chain PFAAs (PFOA, PFOS, and PFNA) is controlled by SPS and dissolved organic carbon (OC), driven by hydrophobic interactions. Additionally, SPS dominates OC transport in estuarine systems, except in sandy sediment environments. SPS plays a dominant role in PFAA partitioning in both surface and bottom water-SPS systems (p < 0.05), and salinity only significantly affects PFBS in bottom layer (p < 0.01). These findings are critical for understanding the drivers of PFAA partitioning and the roles of SPS in different layers, underscoring the necessity of considering particle-associated PFAA fractions in future coastal environmental management.

Conjugation of TLR7 and TLR7/8 agonists onto weak protein antigen via versatile oxime ligation for enhanced vaccine efficacy.

Protein-based subunit vaccines are weakly immunogenic, and developing self-adjuvanting vaccines with adjuvant conjugated to antigen is a promising approach for generating optimal immune responses. Here, we report a novel adjuvant-protein conjugate vaccine based on versatile oxime ligation technique. Firstly, the adjuvant properties of a series of TLR7 and TLR7/8 small molecule agonists in self-adjuvanting vaccines were systematically compared by coupling them to proteins in consistent ratio via p-carboxybenzaldehyde (p-CBA) for the first time. All conjugate vaccines induced cytokine secretion in murine and human macrophages in vitro, and promoted specific antibody production in vivo. Notably, a conjugate containing imidazoquinoline TLR7/8 agonist (TLR7/8a1) showed the greatest enhancement in Th1/2 balanced antibody response. To minimize the interference with the protein antigenic integrity, we further developed a systematic glycoconjugation strategy to conjugate this TLR7/8a1 onto the glycan chains of SARS-CoV-2 S1 glycoprotein via oxime ligation, in which S1 containing different numbers of aldehyde groups were obtained by differential periodate oxidation. The resulting TLR7/8a1-S1 conjugate triggered a potent humoral and cellular immunity in vivo. Together these data demonstrate the promise of these TLR7 and TLR7/8 agonists as effective built-in adjuvants, and the versatile oxime ligation strategy might broaden potential applications in designing different conjugate vaccines.

APLNR inhibited nasopharyngeal carcinoma growth and immune escape by downregulating PD-L1.

BACKGROUND: APLNR is a G protein-coupled receptor and our previous study had revealed that APLNR could inhibit nasopharyngeal carcinoma (NPC) growth and metastasis. However, the role of APLNR in regulating PD-L1 expression and immune escape in NPC is unknown. METHODS: We analyzed the expression and correlation of APLNR and PD-L1 in NPC tissues and cells. We investigated the effect of APLNR on PD-L1 expression and the underlying mechanism in vitro and in vivo. We also evaluated the therapeutic potential of targeting APLNR in combination with PD-L1 antibody in a nude mouse xenograft model. RESULTS: We found that APLNR was negatively correlated with PD-L1 in NPC tissues and cells. APLNR could inhibit PD-L1 expression by binding to the FERM domain of JAK1 and blocking the interaction between JAK1 and IFNGR1, thus suppressing IFN-γ-mediated activation of the JAK1/STAT1 pathway. APLNR could also inhibit NPC immune escape by enhancing IFN-γ secretion and CD8+ T-cell infiltration and reducing CD8+ T-cell apoptosis and dysfunction. Moreover, the best effect was achieved in inhibiting NPC growth in nude mice when APLNR combined with PD-L1 antibody. CONCLUSIONS: Our study revealed a novel mechanism of APLNR regulating PD-L1 expression and immune escape in NPC and suggested that APLNR maybe a potential therapeutic target for NPC immunotherapy.

4-Cyanotryptophan as a Sensitive Fluorescence Probe of Local Electric Field of Proteins.

Electrostatic interactions are key determinants of protein structure, dynamics, and function. Since protein electrostatics are nonuniform, assessment of the internal electric fields (EFs) of proteins requires spatial resolution at the amino acid residue level. In this regard, vibrational Stark spectroscopy, in conjunction with various unnatural amino acid-based vibrational probes, has become a common method for site-specific interrogation of protein EFs. However, application of this method is often limited to proteins with relatively high solubility, due to the intrinsically low oscillator strength of vibrational transitions. Therefore, it would be useful to develop an alternative method that can overcome this limitation. To this end, we show that, using solvatochromic study and molecular dynamics simulations, the frequency of maximum emission intensity of the fluorophore of 4-cyanotryptophan (4CN-Trp), 3-methyl-1H-indole-4-carbonitrile, exhibits a linear dependence on the local EF. Since the absorption and emission spectra of 4CN-Trp are easily distinguishable from those of naturally occurring aromatic amino acids, we believe that this linear relationship provides an easier and more sensitive means to determine the local EF of proteins.

Photophysics of Two Indole-Based Cyan Fluorophores.

For the purpose of searching for new biological fluorophore, we assess the photophysical properties of two indole derivatives, 4-cyano-7-azaindole (4CN7AI) and 1-methyl-4-cyano-7-azaindole (1M4CN7AI), in a series of solvents. We find that (1) the absorption spectra of both derivatives are insensitive to solvents and are red-shifted from that of indole, having a maximum absorption wavelength of ca. 318 nm and a broad profile that extends beyond 370 nm; (2) both derivatives emit in the blue to green spectral range with a large Stokes shift, for example, in H2O, the maximum emission wavelength of 4CN7AI (1M4CN7AI) is at ca. 455 nm (470 nm); (3) 4CN7AI has a higher fluorescence quantum yield (QY) and a longer fluorescence lifetime (τF) in aprotic solvents than in protic solvents, for example, QY (τF) = 0.72 ± 0.04 (7.6 ± 0.8 ns) in tetrahydrofuran and QY (τF) = 0.29 ± 0.03 (6.2 ± 0.6 ns) in H2O; (4) in all of the solvents used except H2O, the fluorescence QY (τF) of 1M4CN7AI is equal to or higher (longer) than 0.69 ± 0.03 (11.2 ± 0.7 ns). Taken together, these results suggest that the corresponding non-natural amino acids, 4-cyano-7-azatryptophan and 1-methyl-4-cyano-7-azatryptophan, could be useful as biological fluorophores.

Metabolic dialogs between B cells and the tumor microenvironment: Implications for anticancer immunity.

Immunometabolism, a branch of biology describing the link between immunity and metabolism, is an emerging topic in cancer immunology. It is currently well accepted that B cells and tertiary lymph structures formed by them are associated with favorable outcomes when patients undergo cancer immunotherapy. Understanding the determinants of B-cell fate and function in cancer patients is necessary for improving cancer immunotherapy. Accumulating evidence points to the tumor microenvironment being a critical metabolic hurdle to an efficient antitumor B-cell response. At the same time, several B-cell-derived metabolites have recently been reported to inhibit anticancer immunity. In this literature review, key B-cell immunometabolism studies and the metabolic life of B cells were summarized. Then, we discussed the intrinsic metabolic pathways of B cells themselves and how the tumor microenvironment and B cells in tumors metabolically influence each other. Finally, we pointed out key questions to provide some inspiration for further study of the role of B-cell immunometabolism in the antitumor immune response.

C≡N Stretching Frequency as a Convenient Reporter of Charge Separation in Molecular Systems.

Previously, several studies have shown that, for a set of structurally related nitrile compounds, there could be a linear relationship between the total charge on the nitrile group (qCN) and its stretching frequency (νCN). However, it is unclear whether the corresponding frequency and charge properties of structurally different nitrile compounds can be described by a single linear νCN-qCN relationship. Herein, we compute the qCN magnitudes of a large number of nitrile-containing molecules whose νCN values cover a spectral range of ca. 200 cm-1 and are measured under different experimental conditions. Our results reveal that νCN indeed exhibits a linear dependence on qCN, with a slope of 637 ± 30 cm-1/charge. Because the nitrile moiety is a commonly used building block in electronic donor-acceptor (D-A) molecular systems, we believe that this linear relationship will find utility in a wide range of applications where such D-A constructs are used, such as in organic photovoltaic assemblies. In addition, we apply this linear relationship to characterize the degree of charge transfer upon photoexcitation of two indole derivatives, 5-cyanoindole and 6-cyanoindole, and are able to show that in both cases, the fluorescence emission arises from a charge-transfer or La state.

Adjuvant-Free COVID-19 Vaccine with Glycoprotein Antigen Oxidized by Periodate Rapidly Elicits Potent Immune Responses.

Modification of antigens to improve their immunogenicity represents a promising direction for the development of protein vaccine. Here, we designed facilely prepared adjuvant-free vaccines in which the N-glycan of SARS-CoV-2 receptor-binding domain (RBD) glycoprotein was oxidized by sodium periodate. This strategy only minimally modifies the glycans and does not interfere with the epitope peptides. The RBD glycoprotein oxidized by high concentrations of periodate (RBDHO) significantly enhanced antigen uptake mediated by scavenger receptors and promoted the activation of antigen-presenting cells. Without any external adjuvant, two doses of RBDHO elicited 324- and 27-fold increases in IgG antibody titers and neutralizing antibody titers, respectively, compared to the unmodified RBD antigen. Meanwhile, the RBDHO vaccine could cross-neutralize all of the SARS-CoV-2 variants of concern. In addition, RBDHO effectively enhanced cellular immune responses. This study provides a new insight for the development of adjuvant-free protein vaccines.

NUCB2: roles in physiology and pathology.

Nucleobindin2 (NUCB2) is a member of nucleobindin family which was first found in the nucleus of the hypothalamus, and had a relationship in diet and energy homeostasis. Its location in normal tissues such as stomach and islet further confirms that it plays a vital role in the regulation of physiological functions of the body. Besides, NUCB2 participates in tumorigenesis through activating various signal-pathways, more and more studies indicate that NUCB2 might impact tumor progression by promoting or inhibiting proliferation, apoptosis, autophagy, metastasis, and invasion of tumor cells. In this review, we comprehensively stated NUCB2's expression and functions, and introduced the role of NUCB2 in physiology and pathology and its mechanism. What is more, pointed out the potential direction of future research.

Photoenhancement of the C≡N Stretching Vibration Intensity of Aromatic Nitriles.

The C≡N stretching vibration is a versatile infrared (IR) reporter that is useful for a wide range of applications. Aiming to further expand its spectroscopic utility, herein, we show that, using 4-cyanoindole and 4-cyano-7-azaindole as examples, photoexcitation can significantly shift the frequency (νCN) and enhance the molar extinction coefficient (εCN) of this vibrational mode of aromatic nitriles and that, for these indole derivatives, the enhancement factor can reach 13. Moreover, we find that while solvent relaxation at the excited electronic state(s) always leads to an increase in εCN, its effect on νCN depends on the solute and the solvent. Taken together, these results demonstrate that solvent relaxation can differently affect the local environment of the nitrile group and its conjugation with the indole ring and, more importantly, that the C≡N stretching vibration can serve as a sensitive IR probe of charge and electron transfer processes in which an aromatic nitrile is involved.