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.

Casein/butyrylated dextrin nanoparticles and chitosan stabilized bilayer emulsions as fat substitutes in sponge cakes.

This study aimed to evaluate the potential of the bilayer emulsions stabilized with casein/butyrylated dextrin nanoparticles and chitosan as fat substitutes in preparing low-calorie sponge cakes. Among the different cake groups, the substitution of bilayer emulsions at 60% exhibited comparable baking properties, appearance, texture characteristics and stable secondary structure to fat. The specific volume and height were increased by 36.94% and 22%, respectively, while the cake showed higher lightness (L*) in the cores and softer hardness in the crumb. In addition, the moisture content of cakes was increased while the water activity remained unchanged. These results showed that casein/butyrylated dextrin bilayer emulsion was a potential fat substitute for cake products at the ratio of 60% with the desirable characteristics.

Development of a clinical nomogram for prediction of response to neoadjuvant chemotherapy in patients with advanced gastric cancer.

BACKGROUND: The efficacy of neoadjuvant chemotherapy (NAC) in advanced gastric cancer (GC) is still a controversial issue. AIM: To find factors associated with chemosensitivity to NAC treatment and to provide the optimal therapeutic strategies for GC patients receiving NAC. METHODS: The clinical information was collected from 230 GC patients who received NAC treatment at the Central South University Xiangya School of Medicine Affiliated Haikou Hospital from January 2016 to December 2020. Least absolute shrinkage and selection operator logistic regression analysis was used to find the possible predictors. A nomogram model was employed to predict the response to NAC. RESULTS: In total 230 patients were finally included in this study, including 154 males (67.0%) and 76 females (33.0%). The mean age was (59.37 ± 10.60) years, ranging from 24 years to 80 years. According to the tumor regression grade standard, there were 95 cases in the obvious response group (grade 0 or grade 1) and 135 cases in the poor response group (grade 2 or grade 3). The obvious response rate was 41.3%. Least absolute shrinkage and selection operator analysis showed that four risk factors significantly related to the efficacy of NAC were tumor location (P < 0.001), histological differentiation (P = 0.001), clinical T stage (P = 0.008), and carbohydrate antigen 724 (P = 0.008). The C-index for the prediction nomogram was 0.806. The calibration curve revealed that the predicted value exhibited good agreement with the actual value. Decision curve analysis showed that the nomogram had a good value in clinical application. CONCLUSION: A nomogram combining tumor location, histological differentiation, clinical T stage, and carbohydrate antigen 724 showed satisfactory predictive power to the response of NAC and can be used by gastrointestinal surgeons to determine the optimal treatment strategies for advanced GC patients.

The rapid proximity labeling system PhastID identifies ATP6AP1 as an unconventional GEF for Rheb.

Rheb is a small G protein that functions as the direct activator of the mechanistic target of rapamycin complex 1 (mTORC1) to coordinate signaling cascades in response to nutrients and growth factors. Despite extensive studies, the guanine nucleotide exchange factor (GEF) that directly activates Rheb remains unclear, at least in part due to the dynamic and transient nature of protein-protein interactions (PPIs) that are the hallmarks of signal transduction. Here, we report the development of a rapid and robust proximity labeling system named Pyrococcus horikoshii biotin protein ligase (PhBPL)-assisted biotin identification (PhastID) and detail the insulin-stimulated changes in Rheb-proximity protein networks that were identified using PhastID. In particular, we found that the lysosomal V-ATPase subunit ATP6AP1 could dynamically interact with Rheb. ATP6AP1 could directly bind to Rheb through its last 12 amino acids and utilizes a tri-aspartate motif in its highly conserved C-tail to enhance Rheb GTP loading. In fact, targeting the ATP6AP1 C-tail could block Rheb activation and inhibit cancer cell proliferation and migration. Our findings highlight the versatility of PhastID in mapping transient PPIs in live cells, reveal ATP6AP1's role as an unconventional GEF for Rheb, and underscore the importance of ATP6AP1 in integrating mTORC1 activation signals through Rheb, filling in the missing link in Rheb/mTORC1 activation.

Interfacial engineering method to regulate the performances of bilayer emulsions co-stabilized by casein/butyrylated dextrin nanoparticles and chitosan.

In present study, bilayer emulsions with different interfacial structures stabilized by casein/butyrylated dextrin nanoparticles (CDNP), chitosan (CS) and chitosan nanoparticles (CSNP) were prepared to overcome the limitations of conventional emulsions. The effects of chitosan morphology and incorporation sequences on the bilayer emulsions were examined. Bilayer emulsions prepared with CDNP as the inner layer and CS/CSNP as the outer layer were observed to have smaller droplet sizes (1.39 ± 86.74 um and 1.45 ± 7.87 um). Bilayer emulsions prepared with CDNP as the inner layer and CS as the outer layer exhibited the lowest creaming index (2.38 %) after 14 days of storage, indicating excellent stability. Furthermore, bilayer emulsion prepared with CDNP as the inner layer and CS as the outer layer also exhibited a uniform water distribution, excellent protein oxidative stability, and uniformly distributed droplets by the measurement of Low-field NMR, intrinsic tryptophan fluorescence and laser confocal laser scanning microscopy. These results indicated that the study provided a theoretical basis for the development and design of bilayer emulsions with different interfacial structures. This study also provides a new material for the preparation of delivery systems that protect biologically active compounds. Bilayer emulsions are promising for applications in traditional and manufactured food products.

KCNH6 is essential for insulin secretion by regulating intracellular ER Ca2+ store.

Appropriate Ca2+ concentration in the endoplasmic reticulum (ER), modulating cytosolic Ca2+ signal, serves significant roles in physiological function of pancreatic ß cells. To maintaining ER homeostasis, Ca2+ movement across the ER membrane is always accompanied by a simultaneous K+ flux in the opposite direction. KCNH6 was proven to modulate insulin secretion by controlling plasma membrane action potential duration and intracellular Ca2+ influx. Meanwhile, the specific function of KCNH6 in pancreatic ß-cells remains unclear. In this study, we found that KCNH6 exhibited mainly ER localization and Kcnh6 ß-cell-specific knockout (ßKO) mice suffered from abnormal glucose tolerance and impaired insulin secretion in adulthood. ER Ca2+ store was overloaded in islets of ßKO mice, which contributed to ER stress and ER stress-induced apoptosis in ß cells. Next, we verified that ethanol treatment induced increases in ER Ca2+ store and apoptosis in pancreatic ß cells, whereas adenovirus-mediated KCNH6 overexpression in islets attenuated ethanol-induced ER stress and apoptosis. In addition, tail-vein injections of KCNH6 lentivirus rescued KCNH6 expression in ßKO mice, restored ER Ca2+ overload and attenuated ER stress in ß cells, which further confirms that KCNH6 protects islets from ER stress and apoptosis. These data suggest that KCNH6 on the ER membrane may help to stabilize intracellular ER Ca2+ stores and protect ß cells from ER stress and apoptosis. In conclusion, our study reveals the protective potential of KCNH6-targeting drugs in ER stress-induced diabetes.

Single-Atom Site SERS Chip for Rapid, Ultrasensitive, and Reproducible Direct-Monitoring of RNA Binding.

Ribonucleic acids (RNA) play active roles within cells or viruses by catalyzing biological reactions, controlling gene expression, and communicating responses to cellular signals. Rapid monitoring RNA variation has become extremely important for appropriate clinical decisions and frontier biological research. However, the most widely used method for RNA detection, nucleic acid amplification, is restricted by a mandatory temperature cycling period of ≈1 h required to reach target detection criteria. Herein, a direct detection approach via single-atom site integrated surface-enhanced Raman scattering (SERS) monitoring nucleic acid pairing reaction, can be completed within 3 min and reaches high sensitivity and extreme reproducibility for COVID-19 and two other influenza viruses' detection. The mechanism is that a single-atom site on SERS chip, enabled by positioning a single-atom oxide coordinated with a specific complementary RNA probe on chip nanostructure hotspots, can effectively bind target RNA analytes to enrich them at designed sites so that the binding reaction can be detected through Raman signal variation. This ultrafast, sensitive, and reproducible single-atom site SERS chip approach paves the route for an alternative technique of immediate RNA detection. Moreover, single-atom site SERS is a novel surface enrichment strategy for SERS active sites for other analytes at ultralow concentrations.

All-potassium channel CRISPR screening reveals a lysine-specific pathway of insulin secretion.

OBJECTIVE: Genome-scale CRISPR-Cas9 knockout coupled with single-cell RNA sequencing (scRNA-seq) has been used to identify function-related genes. However, this method may knock out too many genes, leading to low efficiency in finding genes of interest. Insulin secretion is controlled by several electrophysiological events, including fluxes of KATP depolarization and K+ repolarization. It is well known that glucose stimulates insulin secretion from pancreatic ß-cells, mainly via the KATP depolarization channel, but whether other nutrients directly regulate the repolarization K+ channel to promote insulin secretion is unknown. METHODS: We used a system involving CRISPR-Cas9-mediated knockout of all 83 K+ channels and scRNA-seq in a pancreatic ß cell line to identify genes associated with insulin secretion. RESULTS: The expression levels of insulin genes were significantly increased after all-K+ channel knockout. Furthermore, Kcnb1 and Kcnh6 were the two most important repolarization K+ channels for the increase in high-glucose-dependent insulin secretion that occurred upon application of specific inhibitors of the channels. Kcnh6 currents, but not Kcnb1 currents, were reduced by one of the amino acids, lysine, in both transfected cells, primary cells and mice with ß-cell-specific deletion of Kcnh6. CONCLUSIONS: Our function-related CRISPR screen with scRNA-seq identifies Kcnh6 as a lysine-specific channel.

Social media promotion, risk perception, and parental support for adolescent girls' HPV vaccination: Taking consideration of future consequences and sexual attitudes as moderators.

HPV vaccine hesitancy in Asia is unique compared to western countries. Concerning whether social media promotion about HPV vaccine will be related with parental support for Chinese adolescent girls, we investigated the correlation among social media promotion, risk perception of HPV vaccine and parental support. Through the theoretical lens of Health Action Process Approach model (HAPA), we found that social media promotion could reduce the risk perception of HPV vaccine and promoted parental supportive decision, and risk perception played a mediation role between social media information exposure to vaccine and parental support. Consideration of future consequences has been found to play a moderating role between social media promotion and risk perception, and parents' sexual attitudes moderated the effect of social media promotion on parental support. Implications of the findings are discussed.

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.

The natural compound Sanggenon C inhibits PRRSV infection by regulating the TRAF2/NF-κB signalling pathway.

Porcine reproductive and respiratory syndrome (PRRS) is a serious infectious disease and one of the major causes of death in the global pig industry. PRRS virus (PRRSV) strains have complex and diverse genetic characteristics and cross-protection between strains is low, which complicates vaccine selection; thus, the current vaccination strategy has been greatly compromised. Therefore, it is necessary to identify effective natural compounds for the clinical treatment of PRRS. A small molecule library composed of 720 natural compounds was screened in vitro, and we found that Sanggenon C (SC) was amongst the most effective natural compound inhibitors of PRRSV infection. Compared with ribavirin, SC more significantly inhibited PRRSV infection at both the gene and protein levels and reduced the viral titres and levels of protein expression and inflammatory cytokine secretion to more effectively protect cells from PRRSV infection and damage. Mechanistically, SC inhibits activation of the NF-κB signalling pathway by promoting TRAF2 expression, thereby reducing PRRSV replication. In conclusion, by screening natural compounds, we found that SC suppresses PRRSV infection by regulating the TRAF2/NF-κB signalling pathway. This study contributes to a deeper understanding of the therapeutic targets and pathogenesis of PRRSV infection. More importantly, our results demonstrate that SC has potential as a candidate for the treatment of PRRS.

Integrated single-cell and bulk RNA sequencing analysis identifies a neoadjuvant chemotherapy-related gene signature for predicting survival and therapy in breast cancer.

Neoadjuvant chemotherapy (NAC) is a well-established treatment modality for locally advanced breast cancer (BC). However, it can also result in severe toxicities while controlling tumors. Therefore, reliable predictive biomarkers are urgently needed to objectively and accurately predict NAC response. In this study, we integrated single-cell and bulk RNA-seq data to identify nine genes associated with the prognostic response to NAC: NDRG1, CXCL14, HOXB2, NAT1, EVL, FBP1, MAGED2, AR and CIRBP. Furthermore, we constructed a prognostic risk model specifically linked to NAC. The clinical independence and generalizability of this model were effectively demonstrated. Additionally, we explore the underlying cancer hallmarks and microenvironment features of this NAC response-related risk score, and further assess the potential impact of risk score on drug response. In summary, our study constructed and validated a nine-gene signature associated with NAC prognosis, which was accomplished through the integration of single-cell and bulk RNA data. The results of our study are of crucial significance in the prediction of the efficacy of NAC in BC, and may have implications for the clinical management of this disease.

Developing Ni single-atom sites in carbon nitride for efficient photocatalytic H2O2 production.

Photocatalytic two-electron oxygen reduction to produce high-value hydrogen peroxide (H2O2) is gaining popularity as a promising avenue of research. However, structural evolution mechanisms of catalytically active sites in the entire photosynthetic H2O2 system remains unclear and seriously hinders the development of highly-active and stable H2O2 photocatalysts. Herein, we report a high-loading Ni single-atom photocatalyst for efficient H2O2 synthesis in pure water, achieving an apparent quantum yield of 10.9% at 420 nm and a solar-to-chemical conversion efficiency of 0.82%. Importantly, using in situ synchrotron X-ray absorption spectroscopy and Raman spectroscopy we directly observe that initial Ni-N3 sites dynamically transform into high-valent O1-Ni-N2 sites after O2 adsorption and further evolve to form a key *OOH intermediate before finally forming HOO-Ni-N2. Theoretical calculations and experiments further reveal that the evolution of the active sites structure reduces the formation energy barrier of *OOH and suppresses the O=O bond dissociation, leading to improved H2O2 production activity and selectivity.

Quantum mechanics/molecular mechanics studies on the excited-state decay mechanisms of cytidine aza-analogues: 5-azacytidine and 2'-deoxy-5-azacytidine in aqueous solution.

The excited state properties and deactivation pathways of two DNA methylation inhibitors, i.e., 5-azacytidine (5ACyd) and 2'-deoxy-5-azacytidine (5AdCyd) in aqueous solution, are comprehensively explored with the QM(CASPT2//CASSCF)/MM protocol. We systematically map the feasible decay mechanisms based on the obtained excited-state decay paths involving all the identified minimum-energy structures, conical intersections, and crossing points driving the different internal conversion (IC) and intersystem crossing (ISC) routes in and between the 1ππ*, 1nπ*, 3ππ*, 3nπ*, and S0 states. Unlike the 1nπ* state below the 1ππ* state in 5ACyd, deoxyribose group substitution at the N1 position leads to the 1ππ* state becoming the S1 state in 5AdCyd. In 5ACyd and 5AdCyd, the initially populated 1ππ* state mainly deactivates to the S0 state through the direct 1ππ* → S0 IC or mediated by the 1nπ* state. The former nearly barrierless IC channel of 1ππ* → S0 occurs ultrafast via the nearby low-lying 1ππ*/S0 conical intersection. In the latter IC channel of 1ππ* → 1nπ* → S0, the initially photoexcited 1ππ* state first approaches the nearby S2/S1 conical section 1ππ*/1nπ* and then undergoes efficient IC to the 1nπ* state, followed by the further IC to the initial S0 state via the S1/S0 conical intersection 1nπ*/S0. The 1nπ*/S0 conical intersection is estimated to be located 6.0 and 4.9 kcal mol-1 above the 1nπ* state minimum in 5ACyd and 5AdCyd, respectively, at the QM(CASPT2)/MM level. In addition to the efficient singlet-mediated IC channels, the minor ISC routes would populate 1ππ* to T1(ππ*) through 1ππ* → T1 or 1ππ* → 1nπ* → T1. Relatively, the 1ππ* → 1nπ* → T1 route benefits from the spin-orbit coupling (SOC) of 1nπ*/3ππ* of 8.7 cm-1 in 5ACyd and 10.2 cm-1 in 5AdCyd, respectively. Subsequently, the T1 system will approach the nearby T1/S0 crossing point 3ππ*/S0 driving it back to the S0 state. Given the 3ππ*/S0 crossing point located above the T1 minimum and the small T1/S0 SOC, i.e., 8.4 kcal mol-1 and 2.1 cm-1 in 5ACyd and 6.8 kcal mol-1 and 1.9 cm-1 in 5AdCyd, respectively, the slow T1 → S0 would trap the system in the T1 state for a while. The present work could contribute to understanding the mechanistic photophysics and photochemistry of similar aza-nucleosides and their derivatives.

Noncoding RNA-Mediated High Expression of PFKFB3 Correlates with Poor Prognosis and Tumor Immune Infiltration of Lung Adenocarcinoma.

Background: There is growing evidence showing that 6-phosphofructo-2-kinase (PFKFB3) plays crucial roles in different types of human cancers, including LUAD; however, the specific mechanism by which PFKFB3 plays a role in LUAD remains unclear. Methods: We investigated the expression of PFKFB3 and explored the underlying mechanism as well as the correlation with immune markers using several online datasets, such as Tumor Immune Estimate Resource (TIMER), UALCAN, and the Cancer Genome Atlas (TCGA) databases, miRWalk, Targetscan, MiRDB and starBase database. Western blot and immunohistochemistry analysis were performed to verify the corresponding outcomes. Results: It was shown that the mRNA expression of PFKFB3 was lower in LUAD than in the normal tissues, while its protein expression was not consistent with the mRNA level. The expression of PFKFB3 was correlated with clinicopathological parameters and several signaling pathways. The potential long chain (lnc)RNA/microRNA/PFKFB3 axis and the possible mechanism by which tumor progression in LUAD is promoted was predicted. We obtained the LINC01798/LINC02086/AP000845.1/HAGLR-miR-17-5p-PFKFB3 axis after comprehensive analyses of expression, correlation, and survival. Moreover, the expression of PFKFB3 was positively correlated with immune cells and immune checkpoint expression, including PD-1, PD-L1 and CTLA-4. Conclusion: The present study demonstrated that noncoding RNAs mediated the upregulation of PFKFB3 and was associated with a poor prognosis and immune tumor infiltration in LUAD.

Recycling and Reutilization of Waste Carbon Fiber Reinforced Plastics: Current Status and Prospects.

The extensive use of carbon fiber-reinforced plastics (CFRP) in aerospace, civil engineering, and other fields has resulted in a significant amount of waste, leading to serious environmental issues. Finding appropriate methods for recycling CFRP waste and effectively reusing recycled carbon fibers (rCFs) has become a challenging task. This paper presents an overview of the current status of CFRP waste and provides a systematic review and analysis of recycling technologies. In addition to discussing mechanical recycling, thermal decomposition, and chemical solvent degradation methods, the organic alkali/organic solvent method for recycling resins is also elucidated. By introducing the recycling conditions and outcomes of the organic alkali/organic solvent method, the study highlights its significance as a reference for carbon fiber recycling. Furthermore, the paper reviews the current state of rCFs utilization based on its application domains, focusing on research advancements in fiber composites and cementitious composites. Based on these findings, the paper summarizes the existing research limitations and identifies specific areas that require further attention in recycling techniques and rCFs utilization. Lastly, this review provides a prospect on the future of recycling and reusing CFRP waste.

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.

Highly restricted near-surface permafrost extent during the mid-Pliocene warm period.

Accurate understanding of permafrost dynamics is critical for evaluating and mitigating impacts that may arise as permafrost degrades in the future; however, existing projections have large uncertainties. Studies of how permafrost responded historically during Earth's past warm periods are helpful in exploring potential future permafrost behavior and to evaluate the uncertainty of future permafrost change projections. Here, we combine a surface frost index model with outputs from the second phase of the Pliocene Model Intercomparison Project to simulate the near-surface (~3 to 4 m depth) permafrost state in the Northern Hemisphere during the mid-Pliocene warm period (mPWP, ~3.264 to 3.025 Ma). This period shares similarities with the projected future climate. Constrained by proxy-based surface air temperature records, our simulations demonstrate that near-surface permafrost was highly spatially restricted during the mPWP and was 93 ± 3% smaller than the preindustrial extent. Near-surface permafrost was present only in the eastern Siberian uplands, Canadian high Arctic Archipelago, and northernmost Greenland. The simulations are similar to near-surface permafrost changes projected for the end of this century under the SSP5-8.5 scenario and provide a perspective on the potential permafrost behavior that may be expected in a warmer world.

Characteristics and molecular mechanism of drug-tolerant cells in cancer: a review.

Drug resistance in tumours has seriously hindered the therapeutic effect. Tumour drug resistance is divided into primary resistance and acquired resistance, and the recent study has found that a significant proportion of cancer cells can acquire stable drug resistance from scratch. This group of cells first enters the drug tolerance state (DT state) under drug pressure, and gradually acquires stable drug resistance through adaptive mutations in this state. Although the specific mechanisms underlying the formation of drug tolerant cells (DTCs) remain unclear, various proteins and signalling pathways have been identified as being involved in the formation of DTCs. In the current review, we summarize the characteristics, molecular mechanisms and therapeutic strategies of DTCs in detail.

A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity.

Different anatomical locations of the body skin show differences in their gene expression patterns depending on different origins, and the inherent heterogeneous information can be maintained in adults. However, highly resolvable cellular specialization is less well characterized in different anatomical regions of the skin. Pig is regarded as an excellent model animal for human skin research in view of its similar physiology to human. In this study, single-cell RNA sequencing was performed on pig skin tissues from six different anatomical regions of Chenghua (CH) pigs, with a superior skin thickness trait, and the back site of large white (LW) pigs. We obtained 233,715 cells, representing seven cell types, among which we primarily characterized the heterogeneity of the top three cell types, including smooth muscle cells (SMCs), endothelial cells (ECs), and fibroblasts (FBs). Then, we further identified several subtypes of SMCs, ECs, and FBs, and discovered the expression patterns of site-specific genes involved in some important pathways such as the immune response and extracellular matrix (ECM) synthesis in different anatomical regions. By comparing differentially expressed genes of skin FBs among different anatomical regions, we considered TNN, COL11A1, and INHBA as candidate genes for facilitating ECM accumulation. These findings of heterogeneity in the main skin cell types from different anatomical sites will contribute to a better understanding of inherent skin information and place the potential focus on skin generation, transmission, and transplantation, paving the foundation for human skin priming.