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1.
Mol Pharm ; 2024 Apr 16.
Artigo em Inglês | MEDLINE | ID: mdl-38625027

RESUMO

The blood-brain barrier (BBB) is instrumental in clearing toxic metabolites from the brain, such as amyloid-ß (Aß) peptides, and in delivering essential nutrients to the brain, like insulin. In Alzheimer's disease (AD) brain, increased Aß levels are paralleled by decreased insulin levels, which are accompanied by insulin signaling deficits at the BBB. Thus, we investigated the impact of insulin-like growth factor and insulin receptor (IGF1R and IR) signaling on Aß and insulin trafficking at the BBB. Following intravenous infusion of an IGF1R/IR kinase inhibitor (AG1024) in wild-type mice, the BBB trafficking of 125I radiolabeled Aß peptides and insulin was assessed by dynamic SPECT/CT imaging. The brain efflux of [125I]iodo-Aß42 decreased upon AG1024 treatment. Additionally, the brain influx of [125I]iodoinsulin, [125I]iodo-Aß42, [125I]iodo-Aß40, and [125I]iodo-BSA (BBB integrity marker) was decreased, increased, unchanged, and unchanged, respectively, upon AG1024 treatment. Subsequent mechanistic studies were performed using an in vitro BBB cell model. The cell uptake of [125I]iodoinsulin, [125I]iodo-Aß42, and [125I]iodo-Aß40 was decreased, increased, and unchanged, respectively, upon AG1024 treatment. Further, AG1024 reduced the phosphorylation of insulin signaling kinases (Akt and Erk) and the membrane expression of Aß and insulin trafficking receptors (LRP-1 and IR-ß). These findings reveal that insulin signaling differentially regulates the BBB trafficking of Aß peptides and insulin. Moreover, deficits in IGF1R and IR signaling, as observed in the brains of type II diabetes and AD patients, are expected to increase Aß accumulation while decreasing insulin delivery to the brain, which has been linked to the progression of cognitive decline in AD.

2.
Bioresour Technol ; : 130715, 2024 Apr 17.
Artigo em Inglês | MEDLINE | ID: mdl-38641304

RESUMO

To mitigate the environmental risks posed by the accumulation of antibiotic mycelial dregs (AMDs), this study first attempted over 200 tons of mass production fermentation (MP) using tylosin and spectinomycin mycelial dregs alongside pilot-scale fermentation (PS) for comparison, utilizing the integrated-omics and qPCR approaches. Co-fermentation results showed that both antibiotics were effectively removed in all treatments, with an average removal rate of 92%. Antibiotic resistance gene (ARG)-related metabolic pathways showed that rapid degradation of antibiotics was associated with enzymes that inactivate macrolides and aminoglycosides (e.g., K06979, K07027, K05593). Interestingly, MP fermentations with optimized conditions had more efficient ARGs removal because homogenization permitted faster microbial succession, with more stable removal of antibiotic resistant bacteria and mobile genetic elements. Moreover, Bacillus reached 75% and secreted antioxidant enzymes that might inhibit horizontal gene transfer of ARGs. The findings confirmed the advantages of MP fermentation and provided a scientific basis for other AMDs.

3.
Chemosphere ; 353: 141575, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38430934

RESUMO

Bisphenol A (BPA) in seawater tends to be deposited in coastal sediments. However, its degradation under tidal oscillations has not been explored comprehensively. Hydroxyl radicals (·OH) can be generated through Fe cycling under redox oscillations, which have a strong oxidizing capacity. This study focused on the contribution of Fe-mediated production of ·OH in BPA degradation under darkness. The removal of BPA was investigated by reoxygenating six natural coastal sediments, and three redox cycles were applied to prove the sustainability of the process. The importance of low reactivity Fe(II) in the production of ·OH was investigated, specifically, Fe(II) with carbonate and Fe(II) within goethite, hematite and magnetite. The degradation efficiency of BPA during reoxygenation of sediments was 76.78-94.82%, and the contribution of ·OH ranged from 36.74% to 74.51%. The path coefficient of ·OH on BPA degradation reached 0.6985 and the indirect effect of low reactivity Fe(II) on BPA degradation by mediating ·OH production reached 0.5240 obtained via partial least squares path modeling (PLS-PM). This study emphasizes the importance of low reactivity Fe(II) in ·OH production and provides a new perspective for the role of tidal-induced ·OH on the fate of refractory organic pollutants under darkness.


Assuntos
Compostos Benzidrílicos , Fenóis , Fenóis/metabolismo , Compostos Benzidrílicos/metabolismo , Radical Hidroxila , Compostos Ferrosos , Oxirredução
4.
J Alzheimers Dis ; 2024 Feb 19.
Artigo em Inglês | MEDLINE | ID: mdl-38393902

RESUMO

Background: A strong body of evidence suggests that cerebrovascular pathologies augment the onset and progression of Alzheimer's disease (AD). One distinctive aspect of this cerebrovascular dysfunction is the degeneration of brain pericytes-often overlooked supporting cells of blood-brain barrier endothelium. Objective: The current study investigates the influence of pericytes on gene and protein expressions in the blood-brain barrier endothelium, which is expected to facilitate the identification of pathophysiological pathways that are triggered by pericyte loss and lead to blood-brain barrier dysfunction in AD. Methods: Bioinformatics analysis was conducted on the RNA-Seq expression counts matrix (GSE144474), which compared solo-cultured human blood-brain barrier endothelial cells against endothelial cells co-cultured with human brain pericytes in a non-contact model. We constructed a similar cell culture model to verify protein expression using western blots. Results: The insulin resistance and ferroptosis pathways were found to be enriched. Western blots of the insulin receptor and heme oxygenase expressions were consistent with those observed in RNA-Seq data. Additionally, we observed more than 5-fold upregulation of several genes associated with neuroprotection, including insulin-like growth factor 2 and brain-derived neurotrophic factor. Conclusions: Results suggest that pericyte influence on blood-brain barrier endothelial gene expression confers protection from insulin resistance, iron accumulation, oxidative stress, and amyloid deposition. Since these are conditions associated with AD pathophysiology, they imply mechanisms by which pericyte degeneration could contribute to disease progression.

5.
Bioresour Technol ; 397: 130481, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38395233

RESUMO

Brown algae are rich in biostimulants that not only stimulate the overall development and growth of plants but also have great beneficial effects on the whole soil-plant system. However, alginate, the major component of brown algae, is comparatively difficult to degrade. The cost of preparing alginate oligosaccharides (AOSs) is still too high to produce seaweed fertilizer. In this work, the marine bacterium Vibrio sp. B1Z05 is found to be capable of efficient alginate depolymerization and harbors an extended pathway for alginate metabolism. The B1Z05 extracellular cell-free supernatant exhibited great potential for AOS production at low cost, which, together with cellulase, can efficiently hydrolyze seaweed. The brown algal hydrolysis rates were significantly greater than those of the commercial alginate lyase product CE201, and the obtained seaweed extracts were rich in phytohormones. This work provides a low-cost but efficient strategy for the sustainable production of desirable AOSs and seaweed fertilizer.


Assuntos
Celulase , Feófitas , Alga Marinha , Celulase/metabolismo , Hidrólise , Fertilizantes , Polissacarídeo-Liases/metabolismo , Alga Marinha/metabolismo , Alginatos/metabolismo , Oligossacarídeos/metabolismo
6.
3 Biotech ; 14(1): 29, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38178894

RESUMO

The nitrite efficient utilization microorganism Wickerhamomyces anomalus RZWP01 was identified. Using nitrite and ammonium as the sole nitrogen source, the nitrogen removal rate of W. anomalus RZWP01 was 97.4% and 87.1%, respectively. W. anomalus RZWP01 grew well in the nitrite medium with glucose or xylose as the only carbon source. However, the W. anomalus RZWP01 cannot live on the nitrite medium with lactose, citric acid, and methanol as the only carbon source. The maximal cell concentration occurred in the nitrite medium with glucose as the only carbon source at a C/N ratio of 20 for 48 h, reaching 8.92 × 108 cell mL-1. W. anomalus RZWP01 was the first reported yeast that can efficiently utilize nitrite. The isolation and identification of W. anomalus RZWP01 enriched the microbial resources of nitrite-degrading microorganisms and provided functional microorganisms for the water treatment of sustainable aquaculture.

7.
Nat Microbiol ; 9(2): 434-450, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38233647

RESUMO

A strong correlation between gut microbes and host health has been observed in numerous gut metagenomic cohort studies. However, the underlying mechanisms governing host-microbe interactions in the gut remain largely unknown. Here we report that the gut commensal Christensenella minuta modulates host metabolism by generating a previously undescribed class of secondary bile acids with 3-O-acylation substitution that inhibit the intestinal farnesoid X receptor. Administration of C. minuta alleviated features of metabolic disease in high fat diet-induced obese mice associated with a significant increase in these acylated bile acids, which we refer to as 3-O-acyl-cholic acids. Specific knockout of intestinal farnesoid X receptor in mice counteracted the beneficial effects observed in their wild-type counterparts. Finally, we showed that 3-O-acyl-CAs were prevalent in healthy humans but significantly depleted in patients with type 2 diabetes. Our findings indicate a role for C. minuta and acylated bile acids in metabolic diseases.


Assuntos
Ácidos e Sais Biliares , Diabetes Mellitus Tipo 2 , Humanos , Animais , Camundongos , Clostridiales , Dieta Hiperlipídica
8.
Eur J Pharm Sci ; 192: 106625, 2024 Jan 01.
Artigo em Inglês | MEDLINE | ID: mdl-37918545

RESUMO

Saccharides are a popular group of stabilizers in liquid, frozen and freeze dried protein formulations. The current work reviewed the stabilization mechanisms of three groups of saccharides: (i) Disaccharides, specifically sucrose and trehalose; (ii) cyclodextrins (CDs), a class of cyclic oligosaccharides; and (iii) dextrans, a class of polysaccharides. Compared to sucrose, trehalose exhibits a more pronounced preferential exclusion effect in liquid protein formulations, due to its stronger interaction with water molecules. However, trehalose obtains higher phase separation and crystallization propensity in frozen solutions, resulting in the loss of its stabilization function. In lyophilized formulations, sucrose has a higher crystallization propensity. Besides, its glass matrix is less homogeneous than that of trehalose, thus undermining its lyoprotectant function. Nevertheless, the hygroscopic nature of trehalose may result in high water absorption upon storage. Among all the CDs, the ß form is believed to have stronger interactions with proteins than the α- and γ-CDs. However, the stabilization effect, brought about by CD-protein interactions, is case-by-case - in some examples, such interactions can promote protein destabilization. The stabilization effect of hydroxypropyl-ß-cyclodextrin (HPßCD) has been extensively studied. Due to its amphiphilic nature, it can act as a surface-active agent in preventing interfacial stresses. Besides, it is a dual functional excipient in freeze dried formulations, acting as an amorphous bulking agent and lyoprotectant. Finally, dextrans, when combined with sucrose or trehalose, can be used to produce stable freeze dried protein formulations. A strong stabilization effect can be realized by low molecular weight dextrans. However, the terminal glucose in dextrans yields protein glycation, which warrants extra caution during formulation development.


Assuntos
Ciclodextrinas , Trealose , Trealose/química , Sacarose/química , Ciclodextrinas/química , Dextranos/química , Excipientes/química , Água/química , Liofilização
9.
Biomacromolecules ; 25(1): 238-247, 2024 01 08.
Artigo em Inglês | MEDLINE | ID: mdl-38116793

RESUMO

Chitinase plays a vital role in the efficient biotransformation of the chitin substrate. This study aimed to modify and elucidate the contribution of the relatively conserved residues in the active site architecture of a thermophilic chitinase SsChi18A from Streptomyces sp. F-3 in processive catalysis. The enzymatic activity on colloidal chitin increased to 151%, 135%, and 129% in variants Y286W, E287A, and K186A compared with the wild type (WT). Also, the apparent processive parameter G2/G1 was lower in the variants compared to the WT, indicating the essential role of Tyr-286, Glu-287, and Lys-186 in processive catalysis. Additionally, the enzymatic activity on the crystalline chitin of F48W and double mutants F48W/Y209F and F48W/Y286W increased by 35%, 16%, and 36% compared with that for WT. Molecular dynamics simulations revealed that the driving force of processive catalysis might be related to the changes in interaction energy. This study provided a rational design strategy targeting relatively conserved residues to enhance the catalytic activity of GH18 processive chitinases.


Assuntos
Quitinases , Domínio Catalítico , Quitinases/genética , Quitinases/química , Quitinases/metabolismo , Quitina/química , Simulação de Dinâmica Molecular
10.
Artigo em Inglês | MEDLINE | ID: mdl-37979082

RESUMO

Brewer spent grains (BSGs) are one of the most abundant by-products in brewing industry. Due to microbiological instability and high perishability, the efficient degradation of BSGs is of environmental and economic importance. Streptomyces sp. F-3 could grow in the medium with BSGs as the only carbon and nitrogen source. Proteome mass spectrometry revealed that a GH10 xylanase SsXyn10A could be secreted in large quantities. SsXyn10A showed optimum activity at pH 7.0 and 60 °C. SsXyn10A exhibited excellent thermostability which retained approximately 100% and 58% after incubation for 5 h at 50 and 60 °C. SsXyn10A displayed high activity to beechwood xylan (BX) and wheat arabinoxylan (WAX). SsXyn10A is active against xylotetracose (X4), xylopentose (X5), and xylohexose (X6) to produce main products xylobiose (X2) and xylotriose (X3). Ssxyn10A showed synergistic effects with commercial cellulase on BSGs hydrolyzing into soluble sugar. In addition, the steam explosion pretreatment of BSGs as the substrate produced twice as much reducing sugar as the degradation of the original substrate. This study will contribute to efficient utilization of BSGs and provide a thermostable GH10 xylanase which has potential application in biomass hydrolysis.

11.
J Med Chem ; 66(23): 16109-16119, 2023 12 14.
Artigo em Inglês | MEDLINE | ID: mdl-38019899

RESUMO

Multidrug-resistant Gram-negative bacteria present an urgent and formidable threat to the global public health. Polymyxins have emerged as a last-resort therapy against these 'superbugs'; however, their efficacy against pulmonary infection is poor. In this study, we integrated chemical biology and molecular dynamics simulations to examine how the alveolar lung surfactant significantly reduces polymyxin antibacterial activity. We discovered that lung surfactant is a phospholipid-based permeability barrier against polymyxins, compromising their efficacy against target bacteria. Next, we unraveled the structure-interaction relationship between polymyxins and lung surfactant, elucidating the thermodynamics that govern the penetration of polymyxins through this critical surfactant layer. Moreover, we developed a novel analog, FADDI-235, which exhibited potent activity against Gram-negative bacteria, both in the presence and absence of lung surfactant. These findings shed new light on the sequestration mechanism of lung surfactant on polymyxins and importantly pave the way for the rational design of new-generation lipopeptide antibiotics to effectively treat Gram-negative bacterial pneumonia.


Assuntos
Antibacterianos , Polimixinas , Polimixinas/farmacologia , Antibacterianos/química , Lipopeptídeos , Bactérias , Tensoativos , Pulmão
12.
Biotechnol Biofuels Bioprod ; 16(1): 154, 2023 Oct 18.
Artigo em Inglês | MEDLINE | ID: mdl-37853500

RESUMO

BACKGROUND: Lignocellulose is the most abundant natural biomass resource for the production of biofuels and other chemicals. The efficient degradation of cellulose by cellulases is a critical step for the lignocellulose bioconversion. Understanding the structure-catalysis relationship is vital for rational design of more stable and highly active enzymes. Glycoside hydrolase (GH) family 5 is the largest and most functionally diverse group of cellulases, with a conserved TIM barrel structure. The important roles of the various loop regions of GH5 enzymes in catalysis, however, remain poorly understood. RESULTS: In the present study, we investigated the relationship between the loops surrounding active site architecture and its catalytic efficiency, taking TfCel5A, an enzyme from GH5_2 subfamily of Thermobifida fusca, as an example. Large-scale computational simulations and site-directed mutagenesis experiments revealed that three loops (loop 8, 3, and 7) around active cleft played diverse roles in substrate binding, intermediate formation, and product release, respectively. The highly flexible and charged residue triad of loop 8 was responsible for capturing the ligand into the active cleft. Severe fluctuation of loop 3 led to the distortion of sugar conformation at the - 1 subsite. The wobble of loop 7 might facilitate product release, and the enzyme activity of the mutant Y361W in loop 7 was increased by approximately 40%. CONCLUSION: This study unraveled the vital roles of loops in active site architecture and provided new insights into the catalytic mechanism of the GH5_2 cellulases.

13.
J Chem Inf Model ; 63(20): 6316-6331, 2023 10 23.
Artigo em Inglês | MEDLINE | ID: mdl-37821422

RESUMO

Trichothecenes are highly toxic mycotoxins produced by Fusarium fungi, while TRI101/201 family enzymes play a crucial role in detoxification through acetylation. Studies on the substrate specificity and catalytic kinetics of TRI101/201 have revealed distinct kinetic characteristics, with significant differences observed in catalytic efficiency toward deoxynivalenol, while the catalytic efficiency for T-2 toxin remains relatively consistent. In this study, we used structural bioinformatics analysis and a molecular dynamics simulation workflow to investigate the mechanism underlying the differential catalytic activity of TRI101/201. The findings revealed that the binding stability between trichothecenes and TRI101/201 hinges primarily on a hydrophobic cage structure within the binding site. An intrinsic disordered loop, termed loop cover, defined the evolutionary patterns of the TRI101/201 protein family that are categorized into four subfamilies (V1/V2/V3/M). Furthermore, the unique loop displayed different conformations among these subfamilies' structures, which served to disrupt (V1/V2/V3) or reinforce (M) the hydrophobic cages. The disrupted cages enhanced the water exposure of the hydrophilic moieties of substrates like deoxynivalenol and thereby hindered their binding to the catalytic sites of V-type enzymes. In contrast, this water exposure does not affect substrates like T-2 toxin, which have more hydrophobic substituents, resulting in a comparable catalytic efficiency of both V- and M-type enzymes. Overall, our studies provide theoretical support for understanding the catalytic mechanism of TRI101/201, which shows how an intrinsic disordered loop could impact the protein-ligand binding and suggests a direction for rational protein design in the future.


Assuntos
Toxina T-2 , Tricotecenos , Tricotecenos/química , Tricotecenos/metabolismo , Tricotecenos/toxicidade , Sítios de Ligação , Água
14.
Bioresour Technol ; 387: 129664, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37573975

RESUMO

Microbial-mediated sulfur metabolism is closely related to carbon and nitrogen metabolism in natural biological systems. In this study, the effects of sulfur metabolism on microbial communities and functional enzyme succession were investigated based on integrated multi-omics by adding sulfur-containing compounds to aerobic fermentation systems. Sulfur powder was oxidized to S2O32- and subsequently to SO42- by the microbial sulfur-oxidizing system, which lowered the pH to 7.5 on day 7. The decrease in pH resulted in Planifilum (secreted S8, M17 and M32 proteases) losing its competitive advantage, whereas Novibacillus (secreted M14 and M19 metalloproteases) became dominant. Structural proteomics indicated that the surface of Novibacillus proteases has more negatively charged amino acid residues that help maintain protein stability at low pH. These findings aid understanding of the effects of sulfur metabolism on fermentation and the mechanism of microbial adaptation after pH reduction, providing new perspectives on the optimization of fermentation processes.


Assuntos
Microbiota , Multiômica , Fermentação , Enxofre/metabolismo
15.
Pharmaceutics ; 15(8)2023 Aug 04.
Artigo em Inglês | MEDLINE | ID: mdl-37631300

RESUMO

Blood-brain barrier (BBB) dysfunction is prevalent in Alzheimer's disease and other neurological disorders. Restoring normal BBB function through RNA therapy is a potential avenue for addressing cerebrovascular changes in these disorders that may lead to cognitive decline. Although lipid nanoparticles have been traditionally used as drug carriers for RNA, bicelles have been emerging as a better alternative because of their higher cellular uptake and superior transfection capabilities. Cationic bicelles composed of DPPC/DC7PC/DOTAP at molar ratios of 63.8/25.0/11.2 were evaluated for the delivery of RNA in polarized hCMEC/D3 monolayers, a widely used BBB cell culture model. RNA-bicelle complexes were formed at five N/P ratios (1:1 to 5:1) by a thin-film hydration method. The RNA-bicelle complexes at N/P ratios of 3:1 and 4:1 exhibited optimal particle characteristics for cellular delivery. The cellular uptake of cationic bicelles laced with 1 mol% DiI-C18 was confirmed by flow cytometry and confocal microscopy. The ability of cationic bicelles (N/P ratio 4:1) to transfect polarized hCMEC/D3 with FITC-labeled control siRNA was tested vis-a-vis commercially available Lipofectamine RNAiMAX. These studies demonstrated the higher transfection efficiency and greater potential of cationic bicelles for RNA delivery to the BBB endothelium.

16.
J Mol Graph Model ; 124: 108571, 2023 11.
Artigo em Inglês | MEDLINE | ID: mdl-37487372

RESUMO

Thermophilic enzymes are highly desired in industrial applications due to their efficient catalytic activity at high temperature. However, most enzymes exhibit inferior thermostability and it remains challenging to identify the optimal sites for designing mutations to improve protein stability. To tackle this issue, we integrated topological analysis and all-atom molecular dynamics simulations to efficiently pinpoint the thermally-unstable regions in protein structures. Using a protease CN2S8A as the model, we analyzed the intramolecular hydrogen bonding interactions between adjacent secondary structure elements, and then identified the topological weak spots of CN2S8A where weak hydrogen bonding interactions were formed. To examine the role of these sites in protein structural stability, we designed three virtual mutations at different weak spots and characterized the effects of these mutations on the structural properties of CN2S8A. The results showed that all three mutations increased the protein structural stability. In conclusion, these findings provide a novel method to identify the topological weak spots of proteins, with implications in the rational design of biocatalysts with superior thermostability.


Assuntos
Peptídeo Hidrolases , Engenharia de Proteínas , Engenharia de Proteínas/métodos , Simulação de Dinâmica Molecular , Estabilidade Enzimática , Proteínas/genética , Temperatura
17.
ACS Catal ; 13(12): 8195-8205, 2023 Jun 16.
Artigo em Inglês | MEDLINE | ID: mdl-37342832

RESUMO

Direct bioelectrocatalysis applied in biosensors, biofuel cells, and bioelectrosynthesis is based on an efficient electron transfer between enzymes and electrodes in the absence of redox mediators. Some oxidoreductases are capable of direct electron transfer (DET), while others achieve the enzyme to electrode electron transfer (ET) by employing an electron-transferring domain. Cellobiose dehydrogenase (CDH) is the most-studied multidomain bioelectrocatalyst and features a catalytic flavodehydrogenase domain and a mobile, electron-transferring cytochrome domain connected by a flexible linker. The ET to the physiological redox partner lytic polysaccharide monooxygenase or, ex vivo, electrodes depends on the flexibility of the electron transferring domain and its connecting linker, but the regulatory mechanism is little understood. Studying the linker sequences of currently characterized CDH classes we observed that the inner, mobile linker sequence is flanked by two outer linker regions that are in close contact with the adjacent domain. A function-based definition of the linker region in CDH is proposed and has been verified by rationally designed variants of Neurospora crassa CDH. The effect of linker length and its domain attachment on electron transfer rates has been determined by biochemical and electrochemical methods, while distances between the domains of CDH variants were computed. This study elucidates the regulatory mechanism of the interdomain linker on electron transfer by determining the minimum linker length, observing the effects of elongated linkers, and testing the covalent stabilization of a linker part to the flavodehydrogenase domain. The evolutionary guided, rational design of the interdomain linker provides a strategy to optimize electron transfer rates in multidomain enzymes and maximize their bioelectrocatalytic performance.

18.
Acta Biochim Biophys Sin (Shanghai) ; 55(3): 343-355, 2023 Mar 25.
Artigo em Inglês | MEDLINE | ID: mdl-37143326

RESUMO

Thermal stability is one of the most important properties of enzymes, which sustains life and determines the potential for the industrial application of biocatalysts. Although traditional methods such as directed evolution and classical rational design contribute greatly to this field, the enormous sequence space of proteins implies costly and arduous experiments. The development of enzyme engineering focuses on automated and efficient strategies because of the breakthrough of high-throughput DNA sequencing and machine learning models. In this review, we propose a data-driven architecture for enzyme thermostability engineering and summarize some widely adopted datasets, as well as machine learning-driven approaches for designing the thermal stability of enzymes. In addition, we present a series of existing challenges while applying machine learning in enzyme thermostability design, such as the data dilemma, model training, and use of the proposed models. Additionally, a few promising directions for enhancing the performance of the models are discussed. We anticipate that the efficient incorporation of machine learning can provide more insights and solutions for the design of enzyme thermostability in the coming years.


Assuntos
Engenharia de Proteínas , Estabilidade Enzimática
19.
Front Microbiol ; 14: 1170806, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37228377

RESUMO

Introduction: The Three-River Source Nature Reserve is located in the core area of the Qinghai-Tibetan Plateau, with the alpine swamp, meadow and steppe as the main ecosystem types. However, the microbial communities in these alpine ecosystems, and their carbon and nitrogen degrading metabolic networks and limiting factors remain unclear. Methods: We sequenced the diversity of bacteria and fungi in alpine swamps, meadows, steppes, and their degraded and artificially restored ecosystems and analyzed soil environmental conditions. Results: The results indicated that moisture content had a greater influence on soil microbial community structure compared to degradation and restoration. Proteobacteria dominated in high moisture alpine swamps and alpine meadows, while Actinobacteria dominated in low moisture alpine steppes and artificial grasslands. A metabolic network analysis of carbon and nitrogen degradation and transformation using metagenomic sequencing revealed that plateau microorganisms lacked comprehensive and efficient enzyme systems to degrade organic carbon, nitrogen, and other biological macromolecules, so that the short-term degradation of alpine vegetation had no effect on the basic composition of soil microbial community. Correlation analysis found that nitrogen fixation was strong in meadows with high moisture content, and their key nitrogen-fixing enzymes were significantly related to Sphingomonas. Denitrification metabolism was enhanced in water-deficient habitats, and the key enzyme, nitrous oxide reductase, was significantly related to Phycicoccus and accelerated the loss of nitrogen. Furthermore, Bacillus contained a large number of amylases (GH13 and GH15) and proteases (S8, S11, S26, and M24) which may promote the efficient degradation of organic carbon and nitrogen in artificially restored grasslands. Discussion: This study illustrated the irrecoverability of meadow degradation and offered fundamental information for altering microbial communities to restore alpine ecosystems.

20.
Reprod Toxicol ; 119: 108414, 2023 08.
Artigo em Inglês | MEDLINE | ID: mdl-37245696

RESUMO

Cypermethrin (CYP) has been identified as one kind of endocrine-disrupting chemicals (EDCs) to induce male reproduction damage. This study aimed to investigate the effects and mechanisms of miR-30a-5p on CYP induced apoptosis of TM4 mouse Sertoli cells in vitro. In the present study, 0 µM, 10 µM, 20 µM, 40 µM and 80 µM CYP were used to treat TM4 cells for 24 h. The apoptosis of TM4 cells, the expression level of miR-30a-5p, the protein expressions and the interaction between miR-30a-5p and KLF9 were detected by flow cytometry, quantitative Real-Time PCR, Western blot and luciferase reporter assays. CYP induced apoptosis of TM4 cells, inhibited expression of miR-30a-5p in TM4 cells, and overexpression of miR-30a-5p partially recovered CYP induced cells apoptosis. Furthermore, KLF9 was a potential downstream target of miR-30a-5p predicted by publicly available databases. KLF9 expression level in TM4 cells was significantly elevated after treatment with CYP, and the induction was inhibited by miR-30a-5p mimics transfection. Meanwhile, dual-luciferase reporter assay demonstrated that miR-30a-5p directly targeted KLF9-3'UTR. Moreover, in the presence of CYP, the apoptosis regulator p53 expression was also increased in TM4 cells. Overexpression miR-30a-5p or down-regulation of KLF9 both attenuated the induction of CYP on p53 expression. Overall, the present study demonstrated that miR-30a-5p regulated CYP induced TM4 cells apoptosis by targeting KLF9/p53 axis.


Assuntos
MicroRNAs , Animais , Camundongos , Masculino , MicroRNAs/genética , Células de Sertoli/metabolismo , Proteína Supressora de Tumor p53/genética , Linhagem Celular Tumoral , Proliferação de Células , Apoptose
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