Protein design with a machine-learned potential about backbone designability.

Proteins are fundamental molecules that mediate diverse biological processes, and protein design can shed light on the molecular mechanisms underlying their biological functions. Huang and colleagues have developed a sequence-independent statistical model for de novo protein design using neural networks (NNs) to learn the distribution of backbone structures with minimal side-chain information.

Effect of Different Ethylene Oxide Addition Numbers on the Performance of Polyoxyethylene Tallow Amine as a Pesticide Emulsifier.

Surfactant reduces the surface tension of liquids, resulting in improved emulsion stability, and there is great interest in pesticide additives. Ethoxylate is often used as a pesticide emulsifier. However, the degree of ethoxylation and the existence of dioxane byproducts can significantly affect the performance of emulsifiers. Here, a series of polyoxyethylene tallow amines with the addition of different numbers of ethylene oxide (EO) were synthesized and characterized. Their physical and chemical performances were measured. The ability of POEA as a surfactant to reduce water surface tension and the surface adsorption of molecules were assessed based on the static and dynamic surface tensions. The results show that the surfactant molecules preferentially form a saturated adsorption layer in solution, and the mixed-diffusion-kinetics mechanism dominates the adsorption process. With the increase of the EO addition number, the emulsifying property of POEA increases, while the wetting property gradually decreases and the contact angle increases. These results can provide a basis for the selection of pesticide additives. At the same time, the mechanism of removing dioxane by ethoxylate is described, and a simple and low-consumption method is put forward to reduce the dioxane content. It provides a new idea for the removal of dioxane.

zPoseScore model for accurate and robust protein-ligand docking pose scoring in CASP15.

We introduce a deep learning-based ligand pose scoring model called zPoseScore for predicting protein-ligand complexes in the 15th Critical Assessment of Protein Structure Prediction (CASP15). Our contributions are threefold: first, we generate six training and evaluation data sets by employing advanced data augmentation and sampling methods. Second, we redesign the "zFormer" module, inspired by AlphaFold2's Evoformer, to efficiently describe protein-ligand interactions. This module enables the extraction of protein-ligand paired features that lead to accurate predictions. Finally, we develop the zPoseScore framework with zFormer for scoring and ranking ligand poses, allowing for atomic-level protein-ligand feature encoding and fusion to output refined ligand poses and ligand per-atom deviations. Our results demonstrate excellent performance on various testing data sets, achieving Pearson's correlation R = 0.783 and 0.659 for ranking docking decoys generated based on experimental and predicted protein structures of CASF-2016 protein-ligand complexes. Additionally, we obtain an averaged local distance difference test (lDDT pli = 0.558) of AIchemy LIG2 in CASP15 for de novo protein-ligand complex structure predictions. Detailed analysis shows that accurate ligand binding site prediction and side-chain orientation are crucial for achieving better prediction performance. Our proposed model is one of the most accurate protein-ligand pose prediction models and could serve as a valuable tool in small molecule drug discovery.

Comparison of VTE risk scores in guidelines for VTE diagnosis in nonsurgical hospitalized patients with suspected VTE.

BACKGROUND: The assessment of VTE likelihood with VTE risk scores is essential prior to imaging examinations during VTE diagnostic procedure. Little is known with respect to the disparity of predictive power for VTE diagnosis among VTE risk scores in guidelines for nonsurgical hospitalized patients with clinically suspected VTE. METHODS: A retrospective study was performed to compare the predictive power for VTE diagnosis among the Wells, Geneva, YEARS, PERC, Padua, and IMPROVE scores in the leading authoritative guidelines in nonsurgical hospitalized patients with suspected VTE. RESULTS: Among 3168 nonsurgical hospitalized patients with suspected VTE, VTE was finally excluded in 2733(86.3%) ones, whereas confirmed in 435(13.7%) ones. The sensitivity and specificity resulted from the Wells, Geneva, YEARS, PERC, Padua, and IMPROVE scores were (90.3%, 49.8%), (88.7%, 53.6%), (73.8%, 50.2%), (97.7%,16.9%), (80.9%, 44.0%), and (78.2%, 47.0%), respectively. The YI were 0.401, 0.423, 0.240, 0.146, 0.249, and 0.252 for the Wells, Geneva, YEARS, PERC, Padua, and IMPROVE scores, respectively. The C-index were 0.694(0.626-0.762), 0.697(0.623-0.772), 0.602(0.535-0.669), 0.569(0.486-0.652), 0.607(0.533-0.681), and 0.609(0.538-0.680) for the Wells, Geneva, YEARS, PERC, Padua, and IMPROVE scores, respectively. Consistency was significant in the pairwise comparison of Wells vs Geneva(Kappa 0.753, P = 0.565), YEARS vs Padua(Kappa 0.816, P = 0.565), YEARS vs IMPROVE(Kappa 0.771, P = 0.645), and Padua vs IMPROVE(Kappa 0.789, P = 0.812), whereas it did not present in the other pairs. The YI was improved to 0.304, 0.272, and 0.264 for the PERC(AUC 0.631[0.547-0.714], P = 0.006), Padua(AUC 0.613[0.527-0.700], P = 0.017), and IMPROVE(AUC 0.614[0.530-0.698], P = 0.016), with a revised cutoff of 5 or less, 6 or more, and 4 or more denoting the VTE-likely, respectively. CONCLUSIONS: For nonsurgical hospitalized patients with suspected VTE, the Geneva and Wells scores perform best, the PERC scores performs worst despite its significantly high sensitivity, whereas the others perform intermediately, albeit the absolute predictive power of all isolated scores are mediocre. The predictive power of the PERC, Padua, and IMPROVE scores are improved with revised cutoffs.

Identification of regionalmarkers based on the flavor molecular matrix analysis of sauce-aroma style baijiu.

BACKGROUND: Baijiu is a very complex system and its flavor substances are endogenous, influenced by raw materials, starter, production process, production region and other factors. The production region directly affects the composition of flavor substances and quality of baijiu. However, identification of baijiu region is challenging because the corresponding relationship between the production region and baijiu quality is not clear, and the identification of regionalmarkers is indeterminate. In this study, the differences in volatile components of sauce-aroma style baijiu from four representative regions were investigated. RESULTS: A total of 94 volatile compounds were identified in samples tested. Additionally, it was verified that 35 potential flavor substances had important contributions to the aroma of sauce-aroma style baijiu. Meanwhile, nine potential regionalmarkers were screened through multivariate analysis. Further, based on distribution of volatile compounds and the results of sensory evaluation combined with multivariate analysis, a molecular matrix and correlation network were established according to the results of addition experiments, which showed that six substances had a significant impact on the flavor of the tested samples. CONCLUSION: Six key flavor substances (ethyl octanoate, ethyl 2-methylpropanoate, propyl acetate, ethyl heptanoate, 2-nonanone and butyl hexanoate) were considered as important regionalmarkers to effectively identify the production region of sauce-aroma style baijiu. © 2023 Society of Chemical Industry.

CD47 blockade enhances therapeutic efficacy of cisplatin against lung carcinoma in a murine model.

Cisplatin (CDDP) is the first generation of platinum-based drug and is widely used to treat many cancers due to its potency. The present study aims to explore the effects of CDDP on lung carcinoma and its relationship with macrophage phagocytosis. In in vitro study, murine and human lung cancer cell lines were applied and treated with CDDP, CD47 antibody (aCD47), or CDDP plus aCD47. In in vivo study, a tumor xenograft animal model was treated with CDDP, aCD47, or CDDP plus aCD47. Real-time PCR was applied to determine the mRNA expressions. Enzyme-linked immunosorbent assay (ELISA), Western blotting, and Immunofluorescent staining were applied to determine the protein expressions. Flow cytometry was applied to analyze cell apoptosis, phagocytosis, and specific cell populations. CDDP enhanced the expressions of CD47 in lung cancer cells. Interestingly, the blockage of CD47 enhanced the macrophages' phagocytic activity on the CDDP-treated tumor cells. The treatment of CDDP and aCD47 exhibited anti-tumor effects and prolonged the LLC tumor-bearing mice survival time. Mechanistic studies revealed that the treatment of CDDP and aCD47 regulated the phagocytic activity of macrophage, percentage of CD8+ T cells, and cytokines (tumor growth factor (TGF)-ß, interleukin (IL)12p70, and interferon (IFN)-γ) in the tumor-bearing model. CD47 blockade enhanced therapeutic efficacy of cisplatin against lung carcinoma in vivo and in vitro.

Whether the Research on Ethanol-Water Microstructure in Traditional Baijiu Should Be Strengthened?

Baijiu is a unique and traditional distilled liquor in China. Flavor plays a crucial rule in baijiu. Up to now, the research on the flavor of baijiu has progressed from the identification of volatile compounds to the research on key aroma compounds, but the release mechanism of these characteristic compounds is still unclear. Meanwhile, volatile compounds account for only a tiny fraction, whereas ethanol and water account for more than 98% of the content in baijiu. By summarizing the ethanol-water hydrogen bond structure in different alcoholic beverages, it was found that flavor compounds can affect the association strength of the ethanol-water hydrogen bond, and ethanol-water can also affect the interface distribution of flavor compounds. Therefore, the research on ethanol-water microstructure in baijiu is helpful to realize the simple visualization of adulteration detection, aging determination and flavor release mechanism analysis of baijiu, and further uncover the mystery of baijiu.

SENP1 modulates microglia-mediated neuroinflammation toward intermittent hypoxia-induced cognitive decline through the de-SUMOylation of NEMO.

Intermittent hypoxia (IH)-induced cognition decline is related to the neuroinflammation in microglia. SUMOylation is associated with multiple human diseases, which can be reversed by sentrin/SUMO-specific proteases 1 (SENP1). Herein, we investigated the role of SENP1 in IH-induced inflammation and cognition decline. BV-2 microglial cells and mice were used for inflammatory response and cognition function evaluation following IH treatment. Biochemical analysis and Morris water maze methods were used to elaborate the mechanism of SENP1 in IH impairment. Molecular results revealed that IH induced the inflammatory response, as evidenced by the up-regulation of NF-κB activation, IL-1ß and TNF-α in vitro and in vivo. Moreover, IH decreased the expression of SENP1, and increased the SUMOylation of NEMO, not NF-κB P65. Moreover, SENP1 overexpression inhibited IH-induced inflammatory response and SUMOylation of NEMO. However, the inhibitions were abolished by siRNA-NEMO. In contrast, SENP1 depletion enhanced IH-induced inflammatory response and SUMOylation of NEMO, accompanying with increased latency and reduced dwell time in mice. Overall, the results demonstrated that SENP1 regulated IH-induced neuroinflammation by modulating the SUMOylation of NEMO, thus activating the NF-κB pathway, revealing that targeting SENP1 in microglia may represent a novel therapeutic strategy for IH-induced cognitive decline.

Diversity, enzyme production and antibacterial activity of Bacillus strains isolated from sesame-flavored liquor Daqu.

Daqu provides enzymes and precursors for liquor fermentation, and is the core of liquor fermentation. In this study, 11 Bacillus strains were isolated from sesame-flavored liquor Daqu, which can not only produce protease and amylase, but also have antagonistic effects on common pathogens Escherichia coli and Staphylococcus aureus. According to the gyrA gene phylogeny analysis, these 11 Bacillus strains belong to three species, B1, Y14, Y15, and YPDW9 belong to Bacillus mojavensis, W7, W13, YPDW6, and YPDW12 belong to Bacillus subtilis, and W14, Y5, and YPDW1 belong to Bacillus velezensis. According to the results of random amplified polymorphic DNA (RAPD) typing, there are three strains in Bacillus mojavensis, among which Y14 and Y15 are the same ones. All four Bacillus subtilis strains and three Bacillus velezensis strains are different. The specific primers were used to randomly amplify the biological control genes expressing lipopeptide antibiotics (bioA, bmyB, ituC, fenD, srfAA, srfAB, yngG,and yndJ), and the results showed that antagonistic genes other than fenD gene were amplified in four Bacillus mojavensis strains; Bacillus subtilis amplification was significantly different, but srfAA, bmyB and yndJ genes were all present; All genes were amplified in Bacillus velezensis except YPDW1 without ituC. This research provides new ideas for strengthening Daqu and lays a foundation for improving the quality of liquor.

SENP1-mediated NEMO de-SUMOylation inhibits intermittent hypoxia induced inflammatory response of microglia in vitro.

Among the seven small ubiquitin-like modifier (SUMO)-specific proteases (SENPs), our previous work showed that SENP1 suppressed nuclear factor kappa B (NF-κB) activation and alleviates the inflammatory response in microglia. However, the mechanism is still largely unknown. In this study, western blot analysis and enzyme-linked immunosorbent assay were utilized for evaluating the extent of NF-κB activation and expression of proinflammatory cytokines. qPCR and western blot analysis were performed to detect SENP1 expression. Coimmunoprecipitation followed by western blot analysis was applied to measure the changes in SUMOylation of NF-κB essential modulator (NEMO) and P65 in microglia with or without overexpression of SENP1. As the results, we found that intermittent hypoxia (IH) triggered the activation of NF-κB and upregulated the expression levels of tumor necrosis factor-α and interleukin-6. Interestingly, our data indicated that the SUMOylation of NEMO was enhanced by IH while SUMOylation of P65 was not affected. Further, our data showed that overexpression of SENP1 could decrease the extent of NF-κB activation and inhibit the inflammatory response of microglia through regulating the SUMOylation of NEMO. Collectively, this study presents the first report of the SENP1-controlled de-SUMOylation process of NEMO and its critical role in regulating NF-κB activation and proinflammatory cytokines secretion in microglia cells. This study would benefit for clarifying the role of SENP1 in IH-induced activation of microglia, thus providing potential therapeutic targets for obstructive sleep apnea treatment.

SP1 induced long non-coding RNA LINC00958 overexpression facilitate cell proliferation, migration and invasion in lung adenocarcinoma via mediating miR-625-5p/CPSF7 axis.

BACKGROUND: Increasing evidences have underlined the importance of long non-coding RNAs (lncRNAs) in human malignancies. LINC00958 has been found involved in some cancers. However, the underlying mechanical performance of LINC00958 in lung adenocarcinoma (LAD) has not been explored yet. METHODS: The expression of relevant mRNA and protein were measured by qRT-PCR and western blot assays. EdU, colony formation, TUNEL and transwell assays were performed to investigate the function of LINC00958 on LAD progression. Luciferase reporter, RNA pull down and RIP assays were conducted to investigate the molecular mechanism of relevant RNAs. RESULTS: LINC00958 was found notably overexpressed in LAD, which was associated with the stimulation of its promoter activity induced by SP1. LINC00958 depletion dramatically inhibited LAD cell proliferation, migration and invasion capacities by acting as a miR-625-5p sponge. MiR-625-5p curbed LAD progression via targeting CPSF7 and down-regulating its expression. Mechanically, LINC00958 was identified as a competing endogenous RNA (ceRNA) and positively regulated the expression of CPSF7 via sponging miR-625-5p. CONCLUSIONS: LINC00958 might drive LAD progression via mediating miR-625-5p/CPSF7 axis, indicating the potential of targeting LINC00958 for the treatment of LAD.

The association between pulmonary embolism and the cancer-related genomic alterations in patients with NSCLC.

To date, the association between the acute pulmonary embolism (PE) and the currently existing cancer-related genomic alterations in patients with non-small cell lung cancer (NSCLC) has been understudied. We reviewed patients with a confirmed histopathological diagnosis of NSCLC who underwent computed tomography pulmonary angiography (CTPA) and molecular tests including ALK, ROS1, EGFR, BRAF V600E as well as PD-L1 during the diagnosis of NSCLC, to explore the association between the genomic alterations and PE. The results showed that, for the patients with positive results of genomic alterations, the proportion of positive ALK (13.6%vs8.5%, P<0.001) and PD-L1 (24.7%vs19.9%, P = 0.001) in PE group were more than those in Non-PE group. The patients with positive ALK and PD-L1 had the most (19.0%) and second most (15.4%) incidence of PE among all the patients being studied. A multivariate Logistic regression analysis showed that the positive ALK [1.685(1.065-2.215)(P<0.001)] and PD-L1[1.798(1.137-2.201)(P<0.001)] were correlated with the occurrence of PE. The positive results of ALK and PD-L1 genomic alterations may indicate an increased risk of pulmonary embolism in patients with NSCLC.

An authoritative algorithm most appropriate for the prediction of pulmonary embolism in patients with AECOPD.

BACKGROUND: Contemporarily authoritative algorithms for the prediction of acute pulmonary embolism (PE) comprise the Standard algorithm, the Age-adjusted algorithm, the YEARS algorithm, the PERC algorithm, and the PEGeD algorithm. To date, little is known with respect to which algorithm is most appropriate for the PE prediction in patients with acute exacerbation of chronic obstructive pulmonary disease (AECOPD). METHODS: The patients with AECOPD who underwent the confirmed chest imaging investigations of PE due to the likelihood of PE predicted by the Standard algorithm were retrospectively reviewed. The patients were reassessed by the other four algorithms to reveal which algorithm had the best diagnostic accuracy for the likelihood prediction of PE for patients with AECOPD. RESULTS: The results showed that the PEGeD algorithm(88.6, 80.7, 50.4, 97.0%, 4.591, 0.141, 0.693, 82.1%) performed better overall in the sensitivity, specificity, positive predictive value, negative predictive value, positive likelihood ratio, negative likelihood ratio, Youden index, and diagnostic accuracy, in comparison with the Age-adjusted algorithm (78.6, 74.1, 40.1, 94.0%, 3.034, 0.289, 0.527, 74.9%), the YEARS algorithm (71.4, 76.6, 40.3, 92.4%, 3.051, 0.373, 0.480,75.6%), the PERC algorithm (98.6, 1.6, 18.2, 83.3%, 1.002, 0.875, 0.002, 19.2%). The difference of number of patients who were necessary to undergo chest imaging examinations and missed diagnoses resulted from each algorithm between the PEGeD algorithm and the Standard algorithm, the Age-adjusted algorithm, the YEARS algorithm, as well as the PERC algorithm were [- 789 (- 68.1%), N/A], [- 42 (- 3.6%),-21 (- 1.8%)], [- 3 (- 0.3%),-36 (- 3.1%)],[- 771 (- 66.6%), 21 (1.8%)], respectively. CONCLUSIONS: To date, the PEGeD algorithm is the most appropriate strategy among the authoritative algorithms for the likelihood prediction of pulmonary embolism in patients with AECOPD.

The dynamics of volatile compounds and their correlation with the microbial succession during the traditional solid-state fermentation of Gutian Hong Qu glutinous rice wine.

Gutian Hong Qu glutinous rice wine (GHQW) is a representative alcoholic beverage in China. During its traditional brewing process, multiple strains are involved. However, the roles of these microorganisms, particularly their contributions to aroma formation, are poorly understood. Therefore, in this study, the dynamics of volatile components and microbial succession during the traditional fermentation process of GHQW were monitored, by using HS-SPME-GC/MS and high throughput 16 S rRNA and ITS sequencing techniques. Following a 32-day semi-open solid-state fermentation, massive changes in volatile profile and microbial communities were observed. Based on these, the potential correlations between volatile components and microorganisms during the fermentation were explored by using Pearson correlation analysis. It was revealed that 3 bacterial taxa, including Lactococcus lactis, Burkholderia gladioli and Cronobacter helveticus, and 5 fungal taxa, including Wickerhamomyces anomalus, Saccharomyces cerevisiae, Aspergillus vitricola, Aspergillus penicillioides and Monascus purpureus, showed strong connections with various volatile components. Thus these bacteria and fungi might play crucial roles in volatile components biosynthesis, and thus were preliminary considered as core functional microorganisms for GHQW brewing. The detailed information on the dynamic changes of volatile components and microbial communities throughout GHQW brewing can further expand our understanding of the formation mechanisms of GHQW aroma.

Evaluation of antioxidant peptides generated from Jiuzao (residue after Baijiu distillation) protein hydrolysates and their effect of enhancing healthy value of Chinese Baijiu.

BACKGROUND: Jiuzao is the residue after Bajiu distillation which is usually used as forage for livestock. However, it is not fully utilized yet considering the content of protein remained. The present study aimed to isolate antioxidant peptides from Jiuzao protein hydrolysates, then add these peptides into Baijiu product to enhance the healthy value of Baiju. Meanwhile environmental pollution caused by massive Jiuzao can be mitigated indirectly. RESULTS: Four peptides Ala-Tyr-Ile(Leu) (AYI(L)) and Asp-Arg-Glu-Ile(Leu) (DREI(L)) were identified from Jiuzao protein hydrolysates, the extraction contents of AYI + AYL and DREI + DREL were 896.10 and 110.51 mg kg-1 Jiuzao, respectively. On the one hand, antioxidant activities of these peptides were investigated. For in vitro antioxidant assays, AYI, AYL and DREI exhibited strong capacities in oxygen radical absorbance capacity (ORAC) assay. Furthermore, three levels of four peptides were assessed by 2,2'-azobis(2-methylpropanimidamidine) (AAPH)-induced HepG2 cells model. The results showed that these peptides exerted a degree of antioxidant activities in cells. Meanwhile, selected peptides concentrations according to cell assays remined at effective doses after in vitro digestion. On the other hand, the influence of these four peptides on the characteristic aroma compounds in Baijiu was studied. Most characteristic aroma compounds releases were increased with the addition of peptides. CONCLUSION: In the study, antioxidant activities of peptides were evaluated, the feasibility of utilizing Jiuzao protein hydrolysates to obtain beneficial peptides was also proved. Healthy effect of Baijiu or other food can be increased by adding these functional substances. The findings might contribute to food application and Baijiu industries. © 2019 Society of Chemical Industry.

A fluorescent nanoprobe for 4-ethylguaiacol based on the use of a molecularly imprinted polymer doped with a covalent organic framework grafted onto carbon nanodots.

An efficient and rapid fluorescent nanoprobe is described for the determination of the aroma compound 4-ethylguaiacol (4-EG). A molecularly imprinted polymer was doped with a covalent organic framework (COF) grafted onto carbon nanodots that was prepared by one-pot reverse microemulsion polymerization. Amino groups at the surface of carbon nanodots coordinate to the COFs to produce a strong bond and this warrants thermal and chemical stability of the probe. Remaining free amino groups interact with the phenolic hydroxyl groups of 4-EG through acid-base pairing interactions. The probe, with excitation/emission maxima at 350/440 nm, responds to 4-EG due to the charge transfer to the carbon nanodots. Under optimized conditions, fluorescence drops linearly as the concentrations of 4-EG increase from 0.025 to 1 µg mL-1, with a detection limit of 17 ng mL-1. The probe was applied to the determination of 4-ethylguaiacol in Chinese Baijiu and wine samples after pretreatment by a single dilution step. The recoveries of spiked samples ranged from 78.4to 110.1%. Graphical abstract Schematic presentation of the synthesis of a fluorescent nanoprobe based on molecularly imprinted polymers doped with covalent organic framework grafted onto carbon nanodots. It was used as an efficient and rapid nanoprobe for 4-ethylguaiacol detection with high selectivity and sensitivity.

Interactions between p-Cresol and Ala-Lys-Arg-Ala (AKRA) from Sesame-Flavor-Type Baijiu.

The objective of this study was to investigate the influence of Ala-Lys-Arg-Ala (AKRA), a tetrapeptide newly identified from Chinese Sesame flavor-type Baijiu in our previous work, on its binding ability with aroma compounds. A method using headspace solid-phase microextraction combined with gas chromatography-mass spectrometry (HS-SPME-GC/MS) was employed to determine the corresponding binding ability between different concentrations of AKRA (10 - 1000 µg/L) and aromas in Baijiu. In comparison, the aroma molecules in Baijiu before and after adding AKRA were almost the same; only their volatility was altered, with mostly the esters, alcohols, and phenolic compounds being decreased. Additionally, AKRA slightly changed the whole aroma profile of Baijiu, especially with respect to p-cresol (an off-odor in sesame-flavor-type Baijiu), which was verified by systematic sensory experiments including gas chromatography-olfactometry (GC-O) and odor activity values (OAVs) analysis. The nonvolatile tetrapeptide favored the hydrogen bond interactions with p-cresol, forming the AKRA- p-cresol complex, thus reducing the headspace concentration of phenolic off-flavors as evidenced by HS-SPME-GC/MS, ultraviolet (UV) absorption spectroscopy, and nuclear magnetic resonance spectrum (1H NMR) analysis. Meanwhile, the hydrogen bond interaction was further confirmed with the intermolecular cross-peaks between the carboxyl hydrogen of AKRA and the phenolic hydroxyl of p-cresol by nuclear Overhauser effect spectroscopy (1H-1H NOESY).

Cell wall polysaccharides: before and after autolysis of brewer's yeast.

Brewer's yeast is used in production of beer since millennia, and it is receiving increased attention because of its distinct fermentation ability and other biological properties. During fermentation, autolysis occurs naturally at the end of growth cycle of yeast. Yeast cell wall provides yeast with osmotic integrity and holds the cell shape upon the cell wall stresses. The cell wall of yeast consists of ß-glucans, chitin, mannoproteins, and proteins that cross linked with glycans and a glycolipid anchor. The variation in composition and amount of cell wall polysaccharides during autolysis in response to cell wall stress, laying significant impacts on the autolysis ability of yeast, either benefiting or destroying the flavor of final products. On the other hand, polysaccharides from yeast cell wall show outstanding health effects and are recommended to be used in functional foods. This article reviews the influence of cell wall polysaccharides on yeast autolysis, covering cell wall structure changings during autolysis, and functions and possible applications of cell wall components derived from yeast autolysis.

SENP1 inhibits the IH-induced apoptosis and nitric oxide production in BV2 microglial cells.

To reveal SUMOylation and the roles of Sentrin-specific proteases (SENP)s in microglial cells under Intermittent hypoxia (IH) condition would provide more intensive view of understanding the mechanisms of IH-induced central nervous system (CNS) damage. Hence, in the present study, we detected the expression levels of SENPs in microglial cells under IH and normoxia conditions via RT-PCR assay. We found that SENP1 was significantly down-regulated in cells exposure to IH. Subsequently, the effect of IH for the activation of microglia and the potential roles of SENP1 in the SENP1-overexpressing cell lines were investigated via Western blotting, RT-PCR and Griess assay. The present study demonstrated the apoptosis-inducing and activating role of IH on microglia. In addition, we revealed that the effect of IH on BV-2 including apoptosis, nitric oxide synthase (iNOS) expression and nitric oxide (NO) induction can be attenuated by SENP1 overexpression. The results of the present study are of both theoretical and therapeutic significance to explore the potential roles of SENP1 under IH condition and elucidated the mechanisms underlying microglial survival and activation.

Computational Enzyme Redesign Enhances Tolerance to Denaturants for Peptide C-Terminal Amidation.

The escalating demand for biocatalysts in pharmaceutical and biochemical applications underscores the critical imperative to enhance enzyme activity and durability under high denaturant concentrations. Nevertheless, the development of a practical computational redesign protocol for improving enzyme tolerance to denaturants is challenging due to the limitations of relying solely on model-driven approaches to adequately capture denaturant-enzyme interactions. In this study, we introduce an enzyme redesign strategy termed GRAPE_DA, which integrates multiple data-driven and model-driven computational methods to mitigate the sampling biases inherent in a single approach and comprehensively predict beneficial mutations on both the protein surface and backbone. To illustrate the methodology's effectiveness, we applied it to engineer a peptidylamidoglycolate lyase, resulting in a variant exhibiting up to a 24-fold increase in peptide C-terminal amidation activity under 2.5 M guanidine hydrochloride. We anticipate that this integrated engineering strategy will facilitate the development of enzymatic peptide synthesis and functionalization under denaturing conditions and highlight the role of engineering surface residues in governing protein stability.