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1.
Nat Sci Sleep ; 16: 1153-1168, 2024.
Article in English | MEDLINE | ID: mdl-39131167

ABSTRACT

Purpose: There are currently no ideal indicators for predicting the cardiovascular risk of obstructive sleep apnea (OSA). This study aimed to employ urinary metabolomics to detect early cardiovascular risk in patients with moderate-to-severe OSA. Patients and Methods: Male participants who underwent polysomnography from November 2020 to May 2021 were screened. Clinical data, polysomnography data and urine samples were collected. Untargeted metabolomics analyses of urine were performed. Multivariate analyses and receiver operating characteristic (ROC) curve analyses were subsequently performed to identify potential biomarkers. Associations between metabolites and clinical indicators and cardiovascular risk were examined through linear regression analyses with interaction and mediation analyses. Results: Thirty-six male participants were included in the study, comprising 22 males with moderate-to-severe OSA and 14 age-matched controls, with an average age of 39.6 ± 9.2 years. We identified 65 metabolites in the study, involving pathways including pyrimidine, androgen, estrogen, vitamin B6 and sulfate/sulfite metabolism. Among them, epinephrine sulfate was the most significantly altered metabolite. ROC analyses highlighted that epinephrine sulfate had the highest area under the curve (AUC=0.883) for detecting moderate-to-severe OSA. Epinephrine sulfate was statistically correlated with OSA severity, hypoxia-related indicators (apnea-hypopnea index: r=0.685; oxygen desaturation index: r=0.743, p<0.0001), arterial stiffness (arterial augmentation index: r=0.361, p=0.031) and long-term cardiovascular risk (Framingham cardiovascular risk: r=0.375, p=0.024). Linear regression analysis revealed that epinephrine sulfate was significantly associated with an increased in the Framingham risk (ß = 0.004, 95% CI = 0.000-0.009, p = 0.049), with the effect partly mediated by systolic blood pressure (27.6%) and not moderated by other factors. Additionally, it also significantly associated with the increased in the arterial augmentation index (ß = 0.019, 95% CI = 0.000-0.037, p = 0.046), with the effect fully mediated by blood pressure and not moderated by other indices statistically. Conclusion: There are significant metabolic pathway alterations in moderate-to-severe OSA patients. Urinary epinephrine sulfate markedly predicts early cardiovascular risk in OSA patients.

2.
Int J Food Microbiol ; 423: 110844, 2024 Jul 25.
Article in English | MEDLINE | ID: mdl-39068860

ABSTRACT

Lactic acid bacteria are probiotics in the intestines and have been widely used as natural antioxidants in the food industry. In this study, Enterococcus italicus FM5 with strong antioxidant ability was isolated from fresh milk. The safety evaluation showed that E. italicus FM5 was sensitive to ampicillin, chloramphenicol, erythromycin, vancomycin, rifampicin, and tetracycline, and was not hemolytic. Meanwhile, the whole genome information and biofunctional attributes of this strain were determined and analyzed. Subsequently, E. italicus FM5 was co-cultured with traditional yogurt starters (Streptococcus thermophilus and Lactobacillus bulgaricus) to make fermented milk. The results showed that the addition of E. italicus FM5 could improve the oxygen free radical scavenging ability of the fermented milk, and the scavenging rates of DPPH, ABTS, OH-, and O2- radicals reaching up to 95.54 %, 88.35 %, 93.65 %, and 60.29 %, respectively. Furthermore, the addition of E. italicus FM5 reduced the curd time and improved the water holding capacity of the fermented milk. Besides, the growth of Lb. bulgaricus was significantly promoted when co-cultured with E. italicus FM5, thus the survival cells were increased compared with the traditional fermentation processes. Therefore, this study emphasized the potential to manufacture fermented milk by the co-cultivation of E. italicus with traditional yogurt starters.

3.
Front Genet ; 15: 1356105, 2024.
Article in English | MEDLINE | ID: mdl-39081807

ABSTRACT

Background: Obstructive sleep apnea (OSA) syndrome and nonalcoholic fatty liver disease (NAFLD) have been shown to have a close association in previous studies, but their pathogeneses are unclear. This study explores the molecular mechanisms associated with the pathogenesis of OSA and NAFLD and identifies key predictive genes. Methods: Using the Gene Expression Omnibus (GEO) database, we obtained gene expression profiles GSE38792 for OSA and GSE89632 for NAFLD and related clinical characteristics. Mitochondrial unfolded protein response-related genes (UPRmtRGs) were acquired by collating and collecting UPRmtRGs from the GeneCards database and relevant literature from PubMed. The differentially expressed genes (DEGs) associated with OSA and NAFLD were identified using differential expression analysis. Gene Set Enrichment Analysis (GSEA) was conducted for signaling pathway enrichment analysis of related disease genes. Based on the STRING database, protein-protein interaction (PPI) analysis was performed on differentially co-expressed genes (Co-DEGs), and the Cytoscape software (version 3.9.1) was used to visualize the PPI network model. In addition, the GeneMANIA website was used to predict and construct the functional similar genes of the selected Co-DEGs. Key predictor genes were analyzed using the receiver operating characteristic (ROC) curve. Results: The intersection of differentially expressed genes shared between OSA and NAFLD-related gene expression profiles with UPRmtRGs yielded four Co-DEGs: ASS1, HDAC2, SIRT3, and VEGFA. GSEA obtained the relevant enrichment signaling pathways for OSA and NAFLD. PPI network results showed that all four Co-DEGs interacted (except for ASS1 and HDAC2). Ultimately, key predictor genes were selected in the ROC curve, including HDAC2 (OSA: AUC = 0.812; NAFLD: AUC = 0.729), SIRT3 (OSA: AUC = 0.775; NAFLD: AUC = 0.750), and VEGFA (OSA: AUC = 0.812; NAFLD: AUC = 0.861) (they have a high degree of accuracy in predicting whether a subject will develop two diseases). Conclusion: In this study, four co-expression differential genes for OSA and NAFLD were obtained, and they can predict the occurrence of both diseases. Transcriptional mechanisms involved in OSA and NAFLD interactions may be better understood by exploring these key genes. Simultaneously, this study provides potential diagnostic and therapeutic markers for patients with OSA and NAFLD.

4.
Nano Lett ; 24(31): 9608-9616, 2024 Aug 07.
Article in English | MEDLINE | ID: mdl-39012768

ABSTRACT

Fibers of liquid crystal elastomers (LCEs) as promising artificial muscle show ultralarge and reversible contractile strokes. However, the contractile force is limited by the poor mechanical properties of the LCE fibers. Herein, we report high-strength LCE fibers by introducing a secondary network into the single-network LCE. The double-network LCE (DNLCE) shows considerable improvements in tensile strength (313.9%) and maximum actuation stress (342.8%) compared to pristine LCE. To facilitate the controllability and application, a coiled artificial muscle fiber consisting of DNLCE-coated carbon nanotube (CNT) fiber is prepared. When electrothermally driven, the artificial muscle fiber outputs a high actuation performance and programmable actuation. Furthermore, by knitting the artificial muscle fibers into origami structures, an intelligent gripper and crawling inchworm robot have been demonstrated. These demonstrations provide promising application scenarios for advanced intelligent systems in the future.

5.
Plant J ; 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38924231

ABSTRACT

Due to the chelation of phosphorus in the soil, it becomes unavailable for plant growth and development. The mechanisms by which phosphorus-solubilizing bacteria activate immobilized phosphorus to promote the growth and development of woody plants, as well as the intrinsic molecular mechanisms, are not clear. Through the analysis of microbial communities in the rhizosphere 16S V3-V4 and a homologous gene encoding microbial alkaline phosphomonoesterase (phoD) in phosphate-efficient (PE) and phosphate-inefficient apple rootstocks, it was found that PE significantly enriched beneficial rhizobacteria. The best phosphorus-solubilizing bacteria, Bacillus sp. strain 7DB1 (B2), was isolated, purified, and identified from the rhizosphere soil of PE rootstocks. Incubating with Bacillus B2 into the rhizosphere of apple rootstocks significantly increased the soluble phosphorus and flavonoid content in the rhizosphere soil. Simultaneously, this process stimulates the root development of the rootstocks and enhances plant phosphorus uptake. After root transcriptome sequencing, candidate transcription factor MhMYB15, responsive to Bacillus B2, was identified through heatmap and co-expression network analysis. Yeast one-hybrid, electrophoretic mobility shift assay, and LUC assay confirmed that MhMYB15 can directly bind to the promoter regions of downstream functional genes, including chalcone synthase MhCHS2 and phosphate transporter MhPHT1;15. Transgenic experiments with MhMYB15 revealed that RNAi-MhMYB15 silenced lines failed to induce an increase in flavonoid content and phosphorus levels in the roots under the treatment of Bacillus B2, and plant growth was slower than the control. In conclusion, MhMYB15 actively responds to Bacillus B2, regulating the accumulation of flavonoids and the uptake of phosphorus, thereby influencing plant growth and development.

6.
IUBMB Life ; 2024 Jun 27.
Article in English | MEDLINE | ID: mdl-38935610

ABSTRACT

Type 2 diabetes mellitus is a prevalent metabolic disease, posing a considerable threat to public health. Oligonucleotide drugs have proven to be a promising field of therapy for the diseases. In this study, we reported that a herbal small RNA (sRNA), JGL-sRNA-h7 (B34735529, F1439.L002444.A11), could exhibit potent hypoglycemic effects by targeting glucose-6-phosphatase. Oral administration of sphingosine (d18:1)-JGL-sRNA-h7 bencaosomes ameliorated hyperglycemia and diabetic kidney injury better than metformin in db/db mice. Furthermore, glucose tolerance was also improved in sphingosine (d18:1)-JGL-sRNA-h7 bencaosomes-treated beagle dogs. Our study indicates that JGL-sRNA-h7 could be a promising hypoglycemic oligonucleotide drug.

7.
Small ; : e2403062, 2024 Jun 28.
Article in English | MEDLINE | ID: mdl-38940238

ABSTRACT

Aqueous Zn-ion batteries (ZIBs) are considered to be one of the most promising energy storage devices in the post-lithium-ion era with fast ionic conductivity, safety, and low cost. However, excessive accumulation of zinc dendrites will fracture and produce dead zinc, resulting in the unsatisfied utilization rate of Zn anodes, which greatly restricts the lifespan of the battery and reduces the reversibility. In this paper, by constructing a protective layer of ZnSnO3 hollow nanospheres in situ growth on the surface of the Zn anode, more zincophilic sites are established on the electrode surface. It demonstrates that uniform deposition of Zn ions by deepening the binding energy with Zn ion and its unique hollow structure shortens the diffusion distance of Zn ions and enhances the reaction kinetics. The assembled Zn-ion hybrid supercapacitor (ZHSC) of ZnSnO3@Zn//AC achieved a long-term lifespan with 4000 cycles at a current density of 10 mA cm-2 with a Coulombic efficiency of 99.31% and capacity retention of 79.6%. This work offers a new path for advanced Zn anodes interphase supporting the long cycle life with large capacities and improving electrochemical reversibility.

8.
BMC Complement Med Ther ; 24(1): 243, 2024 Jun 22.
Article in English | MEDLINE | ID: mdl-38909225

ABSTRACT

BACKGROUND: Cucurbita pepo cv Dayangua (CPD) is an edible plant with diverse pharmacological properties. The current research on CPD has primarily focused on initial investigations of its chemical composition and pharmacological effects, and no comprehensive toxicity assessment has been conducted to date. METHODS: In the present study, the toxicity of CPD was evaluated through both acute and sub-chronic oral toxicity tests in mice. 16S rDNA sequencing was used to analyze the composition of the gut microbiota of mice at different time points to observe the effect of CPD on these microbial communities. RESULTS: In the acute toxicity test, CPD exhibited low toxicity, with a median lethal dose (LD50) > 2000 mg/kg. The sub-chronic toxicity test indicated that CPD administration at doses of 200, 400, and 600 mg/kg did not cause mortality or significant organ damage in mice. Furthermore, analysis of the gut microbiota after gavage administration of CPD at 400 and 600 mg/kg revealed an improved abundance of some beneficial gut bacteria. CONCLUSIONS: In summary, no acute or sub-chronic toxic effects were observed in mice following the oral administration of CPD. CPD did not affect the structure and diversity of the gut microbiota and may contribute to an increase in the number of beneficial gut bacteria.


Subject(s)
Cucurbita , Gastrointestinal Microbiome , Animals , Gastrointestinal Microbiome/drug effects , Mice , Male , Plant Extracts/pharmacology , Plant Extracts/toxicity , Female , Toxicity Tests, Acute
10.
Front Mol Biosci ; 11: 1339973, 2024.
Article in English | MEDLINE | ID: mdl-38845779

ABSTRACT

Background: In recent years, the incidence of insulin resistance is increasing, and it can cause a variety of Metabolic syndrome. Ginsenosides have been clinically proven to improve fat metabolism and reduce insulin resistance, but their components and mechanism of action are still unclear. Objective: Ginsenoside, a bioactive compound derived from ginseng, exhibits significant potential in treating obesity, diabetes, and metabolic disorders. Despite evidence supporting its efficacy in ameliorating insulin resistance (IR) in obesity, the specific bioactive components and underlying mechanisms remain obscure. In this study, we endeavored to elucidate the potential molecular targets and pathways influenced by ginsenoside Rh3 (GRh3) to ameliorate IR in liver tissue. We employed a comprehensive approach that integrates system pharmacology and bioinformatics analysis. Materials and methods: Our methodology involved the identification of candidate targets for GRh3 and the profiling of differentially expressed genes (DEGs) related to IR in individuals with insulin resistance. The coalescence of candidate targets and DEGs facilitated the construction of a "GRh3-targets-disease" network for each tissue type, ultimately yielding 38 shared target genes. Subsequently, we conducted pathway enrichment analysis, established protein-protein interaction (PPI) networks, and identified hub targets among the GRh3 targets and IR-related DEGs. Additionally, we conducted animal experiments to corroborate the role of these hub targets in the context of GRh3. Results: Our investigation identified a total of 38 overlapping targets as potential candidates. Notably, our analysis revealed crucial hub targets such as EGFR, SRC, ESR1, MAPK1, and CASP3, alongside implicated signaling pathways, including those related to insulin resistance, the FoxO signaling pathway, the PPAR signaling pathway, and the IL-17 signaling pathway. This study establishes a robust foundation for the mechanisms underlying GRh3's efficacy in mitigating IR. Furthermore, these results suggest that GRh3 may serve as a representative compound within the ginsenoside family. Conclusion: This study elucidates the potential molecular targets and associated pathways through which GRh3 ameliorates IR, showcasing its multifaceted nature, spanning multiple targets, pathways, and mechanisms. These findings establish a robust foundation for subsequent experimental inquiries and clinical applications.

11.
BMC Plant Biol ; 24(1): 565, 2024 Jun 15.
Article in English | MEDLINE | ID: mdl-38879490

ABSTRACT

BACKGROUND: AP2/ERF is a large family of plant transcription factor proteins that play essential roles in signal transduction, plant growth and development, and responses to various stresses. The AP2/ERF family has been identified and verified by functional analysis in various plants, but so far there has been no comprehensive study of these factors in Chinese prickly ash. Phylogenetic, motif, and functional analyses combined with transcriptome analysis of Chinese prickly ash fruits at different developmental stages (30, 60, and 90 days after anthesis) were conducted in this study. RESULTS: The analysis identified 146 ZbAP2/ERF genes that could be classified into 15 subgroups. The motif analysis revealed the presence of different motifs or elements in each group that may explain the functional differences between the groups. ZbERF13.2, ZbRAP2-12, and ZbERF2.1 showed high levels of expression in the early stages of fruit development. ZbRAP2-4, and ZbERF3.1 were significantly expressed at the fruit coloring stage (R2 and G2). ZbERF16 were significantly expressed at fruit ripening and expression level increased as the fruit continued to develop. Relative gene expression levels of 6 representative ZbAP2/ERFs assessed by RT-qPCR agreed with transcriptome analysis results. CONCLUSIONS: These genes identified by screening can be used as candidate genes that affect fruit development. The results of the analysis can help guide future genetic improvement of Chinese prickly ash and enrich our understanding of AP2/ERF transcription factors and their regulatory functions in plants.


Subject(s)
Fruit , Gene Expression Regulation, Plant , Phylogeny , Plant Proteins , Transcription Factors , Fruit/genetics , Fruit/growth & development , Plant Proteins/genetics , Plant Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Gene Expression Profiling , Genome, Plant , Genes, Plant , East Asian People
12.
Sleep Breath ; 2024 Jun 17.
Article in English | MEDLINE | ID: mdl-38884695

ABSTRACT

PURPOSE: Chemosensitivity is an essential part of the pathophysiological mechanisms of obstructive sleep apnea (OSA). This study aims to use the rebreathing method to assess hypercapnic ventilatory response (HCVR) and analyze the association between chemosensitivity and certain symptoms in patients with OSA. METHODS: A total of 104 male patients with diagnosed OSA were enrolled. The HCVR was assessed using rebreathing methods under hypoxia exposure to reflect the overall chemosensitivity. Univariate and multivariate linear regression were used to explore the association with chemosensitivity. Participants were enrolled in the cluster analysis using certain symptoms, basic characteristics, and polysomnographic indices. RESULTS: At similar baseline values, the high chemosensitivity group (n = 39) demonstrated more severe levels of OSA and nocturnal hypoxia than the low chemosensitivity group (n = 65). After screening the possible associated factors, nocturnal urination, rather than OSA severity, was found to be positively associated with the level of chemosensitivity. Cluster analysis revealed three distinct groups: Cluster 1 (n = 32, 34.0%) held younger, obese individuals with nocturnal urination, elevated chemosensitivity level, and very severe OSA; Cluster 2 (41, 43.6%) included middle-aged overweighted patients with nocturnal urination, increased chemosensitivity level, but moderate-severe OSA; and Cluster 3 (n = 21, 22.3%) contained middle-aged overweighted patients without nocturnal urination, with a lowered chemosensitivity level and only moderate OSA. CONCLUSION: The presence of nocturnal urination in male patients with OSA may be a sign of higher levels of ventilatory chemosensitivity, requiring early therapy efforts independent of AHI levels.

13.
Virulence ; 15(1): 2368080, 2024 Dec.
Article in English | MEDLINE | ID: mdl-38899573

ABSTRACT

Dendritic cells (DCs) present an ideal target for delivering immunogenic cargo due to their potent antigen-presenting capabilities. This targeting approach holds promise in vaccine development by enhancing the efficiency of antigen recognition and capture by DCs. To identify a high-affinity targeting peptide binding to rabbit DCs, rabbit monocyte-derived DCs (raMoDCs) were isolated and cultured, and a novel peptide, HS (HSLRHDYGYPGH), was identified using a phage-displayed peptide library. Alongside HS, two other DC-targeting peptides, KC1 and MY, previously validated in our laboratory, were employed to construct recombinant Lactgobacillus reuteri fusion-expressed rabbit hemorrhagic disease virus (RHDV) capsid protein VP60. These recombinant Lactobacillus strains were named HS-VP60/L. reuteri, KC1-VP60/L. reuteri, and MY-VP60/L. reuteri. The ability of these recombinant Lactobacillus to bind rabbit DCs was evaluated both in vivo and in vitro. Results demonstrated that the DC-targeting peptide KC1 significantly enhanced the capture efficiency of recombinant Lactobacillus by raMoDCs, promoted DC maturation, and increased cytokine secretion. Furthermore, oral administration of KC1-VP60/L. reuteri effectively induced SIgA and IgG production in rabbits, prolonged rabbit survival post-challenge, and reduced RHDV copies in organs. In summary, the DC-targeting peptide KC1 exhibited robust binding to raMoDCs, and recombinant Lactobacillus expressing KC1-VP60 protein antigens efficiently induced systemic and mucosal immune responses in rabbits, conferring protective efficacy against RHDV. This study offers valuable insights for the development of novel RHDV vaccines.


Subject(s)
Dendritic Cells , Hemorrhagic Disease Virus, Rabbit , Limosilactobacillus reuteri , Peptides , Animals , Dendritic Cells/immunology , Rabbits , Hemorrhagic Disease Virus, Rabbit/immunology , Hemorrhagic Disease Virus, Rabbit/genetics , Limosilactobacillus reuteri/genetics , Limosilactobacillus reuteri/immunology , Peptides/immunology , Peptides/genetics , Caliciviridae Infections/prevention & control , Caliciviridae Infections/immunology , Reoviridae Infections/prevention & control , Reoviridae Infections/immunology , Capsid Proteins/genetics , Capsid Proteins/immunology , Viral Vaccines/immunology , Viral Vaccines/genetics , Lactobacillus/genetics , Lactobacillus/immunology
14.
Comput Biol Med ; 178: 108687, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38870722

ABSTRACT

High-precise modulation of bio-functional proteins related to signaling is crucial in life sciences and human health. The cutting-edge technology of optogenetics, which combines optical method with genetically encoded protein expression, pioneered new pathways for the control of cellular bio-functional proteins (CPs) using optogenetic tools (OTs) in spatial and temporal. Over the past decade, hundreds of optogenetic systems (OSs) have been developed for various applications from living cells to freely moving organisms. However, no database has been constructed to comprehensively provide the valuable information of OSs yet. In this work, a new database named OPTICS (an interactive online platform for photosensory and bio-functional proteins in optogenetic systems) is introduced. Our OPTICS is unique in (i) systematically describing diverse OSs from the perspective of photoreceptor-based classification and mechanism of action, (ii) featuring the detailed biophysical properties and functional data of OSs, (iii) providing the interaction between OT and CP for each OS referring to distinct applications in research, diagnosis, and therapy, and (iv) enabling a light response property-based search against all OSs in the database. Since the information on OSs is essential for rapid and predictable design of optogenetic controls, the comprehensive data provided in OPTICS lay a solid foundation for the future development of novel OSs. OPTICS is freely accessible without login requirement at https://idrblab.org/optics/.


Subject(s)
Optogenetics , Optogenetics/methods , Humans , Animals , Databases, Protein
15.
Intervirology ; 67(1): 72-82, 2024.
Article in English | MEDLINE | ID: mdl-38934174

ABSTRACT

INTRODUCTION: This study aimed to investigate the differences between pregnant women with chronic hepatitis B virus (HBV) infection and intrafamilial infection and those without intrafamilial infection. METHODS: HBV-DNA was extracted from the sera of 16 pregnant women with chronic hepatitis B (CHB) and their family members for gene sequencing and phylogenetic analyses. A total of 74 pregnant women with CHB were followed up from the second trimester to 3 months postpartum. Viral markers and other laboratory indicators were compared between pregnant women with CHB with and without intrafamilial infection. RESULTS: The phylogenetic tree showed that HBV lines in the mother-spread pedigree shared a node, whereas there was an unrelated genetic background for HBV lines in individuals without intrafamilial infection. From delivery to 3 months postpartum, compared with those without intrafamilial infection, pregnant women with intrafamilial infection were related negatively to HBV-DNA (ß = -0.43, 95% confidence interval [CI]: -0.76 to -0.12, p = 0.009), HBeAg (ß = -195.15, 95% CI: -366.35 to -23.96, p = 0.027), and hemoglobin changes (ß = -8.09, 95% CI: -15.54 to -0.64, p = 0.035) and positively to changes in the levels of alanine aminotransferase (ß = 73.9, 95% CI: 38.92-108.95, p < 0.001) and albumin (ß = 2.73, 95% CI: 0.23-5.23, p = 0.033). CONCLUSION: The mother-spread pedigree spread model differs from that of non-intrafamilial infections. Pregnant women with intrafamilial HBV infection have less hepatitis flares and liver damage, but their HBV-DNA and HBeAg levels rebound faster after delivery, than those without intrafamilial infection by the virus.


Subject(s)
DNA, Viral , Hepatitis B virus , Hepatitis B, Chronic , Phylogeny , Pregnancy Complications, Infectious , Humans , Female , Pregnancy , Hepatitis B, Chronic/virology , Hepatitis B virus/genetics , Hepatitis B virus/classification , Adult , DNA, Viral/genetics , DNA, Viral/blood , Pregnancy Complications, Infectious/virology , Hepatitis B e Antigens/blood , Young Adult , Infectious Disease Transmission, Vertical , Genotype , Sequence Analysis, DNA
17.
Nucleic Acids Res ; 52(W1): W272-W279, 2024 Jul 05.
Article in English | MEDLINE | ID: mdl-38738624

ABSTRACT

Protein scaffolds with small size, high stability and low immunogenicity show important applications in the field of protein engineering and design. However, no relevant computational platform has been reported yet to mining such scaffolds with the desired properties from massive protein structures in human body. Here, we developed PROSCA, a structure-based online platform dedicated to explore the space of the entire human proteome, and to discovery new privileged protein scaffolds with potential engineering value that have never been noticed. PROSCA accepts structure of protein as an input, which can be subsequently aligned with a certain class of protein structures (e.g. the human proteome either from experientially resolved or AlphaFold2 predicted structures, and the human proteins belonging to specific families or domains), and outputs humanized protein scaffolds which are structurally similar with the input protein as well as other related important information such as families, sequences, structures and expression level in human tissues. Through PROSCA, the user can also get excellent experience in visualizations of protein structures and expression overviews, and download the figures and tables of results which can be customized according to the user's needs. Along with the advanced protein engineering and selection technologies, PROSCA will facilitate the rational design of new functional proteins with privileged scaffolds. PROSCA is freely available at https://idrblab.org/prosca/.


Subject(s)
Protein Engineering , Software , Humans , Protein Engineering/methods , Proteins/chemistry , Proteins/genetics , Proteome , Models, Molecular , Internet , Protein Conformation
18.
Environ Res ; 255: 119158, 2024 Aug 15.
Article in English | MEDLINE | ID: mdl-38763279

ABSTRACT

The reliable and efficient nitrite production rate (NPR) through nitritation process is the prerequisite for the efficient running of subsequent processes, like the anammox process and the nitrite shunt. However, there has been scant research on stable and productive nitritation process in recent years. In this study, at a stable hydraulic retention time of 12.0 h and with precise and strict DO control, the upper limit of the NPR was initially investigated using a continuous-flow granular sludge reactor. The NPR of 1.69 kg/m3/d with a nitrite production efficiency of 81.97% was finally achieved, which set a record until now in similar research. The median sludge particle size of 270.0 µm confirmed the development of clearly defined granular sludge. The genus Nitrosomonas was the major ammonium oxidizing bacteria. In conclusion, this study provides valuable insights for the practical application of the effective nitritation process driving subsequent nitrogen removal processes.


Subject(s)
Bioreactors , Nitrites , Nitrogen , Sewage , Sewage/microbiology , Nitrites/metabolism , Bioreactors/microbiology , Nitrogen/metabolism , Oxidation-Reduction , Waste Disposal, Fluid/methods , Anaerobiosis , Nitrosomonas/metabolism , Ammonium Compounds/metabolism
19.
Plant Physiol Biochem ; 212: 108767, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38797009

ABSTRACT

Salt stress is a critical limiting factor for fruit yield and quality of apples. Brassinosteroids (BRs) play an important role in response to abiotic stresses. In the present study, application of 2,4- Epicastasterone on seedlings of Malus 'M9T337' and Malus domestica 'Gala3' alleviated the physiological effects, such as growth inhibition and leaf yellowing, induced by salt stress. Further analysis revealed that treatment with NaCl induced expression of genes involved in BR biosynthesis in 'M9T337' and 'Gala3'. Among which, the expression of BR biosynthetic gene MdBR6OX2 showed a three-fold upregulation upon salt treatment, suggesting its potential role in response to salt stress in apple. MdBR6OX2, belonging to the CYP450 family, contains a signal peptide region and a P450 domain. Expression patterns analysis showed that the expression of MdBR6OX2 can be significantly induced by different abiotic stresses. Overexpressing MdBR6OX2 enhanced the tolerance of apple callis to salt stress, and the contents of endogenous BR-related compounds, such as Typhastero (TY), Castasterone (CS) and Brassinolide (BL) were significantly increased in transgenic calli compared with that of wild-type. Extopic expression of MdBR6OX2 enhanced tolerance to salt stress in Arabidopsis. Genes associated with salt stress were significantly up-regulated, and the contents of BR-related compounds were significantly elevated under salt stress. Our data revealed that BR-biosynthetic gene MdBR6OX2 positively regulates salt stress tolerance in both apple calli and Arabidopsis.


Subject(s)
Arabidopsis , Brassinosteroids , Gene Expression Regulation, Plant , Malus , Plant Proteins , Salt Tolerance , Malus/genetics , Malus/metabolism , Malus/drug effects , Brassinosteroids/metabolism , Brassinosteroids/biosynthesis , Brassinosteroids/pharmacology , Arabidopsis/genetics , Arabidopsis/metabolism , Arabidopsis/drug effects , Salt Tolerance/genetics , Gene Expression Regulation, Plant/drug effects , Plant Proteins/genetics , Plant Proteins/metabolism , Plants, Genetically Modified , Salt Stress/genetics , Cytochrome P-450 Enzyme System/genetics , Cytochrome P-450 Enzyme System/metabolism
20.
Org Biomol Chem ; 22(21): 4264-4268, 2024 May 29.
Article in English | MEDLINE | ID: mdl-38742913

ABSTRACT

Herein, we describe a novel metal-free Brønsted acid-catalyzed Ficini [2 + 2] cycloaddition of ynamides with enones under mild reaction conditions, leading to the formation of various cyclobutenamides in generally good to excellent yields within short reaction times. This work represents the first example of ynamides involved in a nonmetal-catalyzed [2 + 2] cycloaddition with enones.

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