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1.
Poult Sci ; 103(8): 103852, 2024 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-38861843

RESUMO

The objective of this study was to determine the effects of dietary crude protein (CP) levels on intestinal antioxidant status, tight junction proteins expression, and amino acids transporters levels in squabs. A total of 180 pairs of White King parent pigeons approximately 10 mo old were randomly assigned to 5 groups with 6 replications of 6 pairs of parental pigeons each, and were fed with 14, 15, 16, 17, and 18% CP diets for 46 d, respectively. Dietary increasing CP levels increased final body weight (linear and quadratic, P < 0.05), serum urea nitrogen (linear, P<0.05) and triglyceride levels (quadratic, P < 0.05), and reduced kidney relative weight (quadratic, P < 0.05) in squabs. Final body weight of squabs in the 18% CP diet group was higher than that of the 14, 15, and 16% CP diet groups (P < 0.05) but was similar to that of the 17% CP diet group (P > 0.05). Increasing dietary CP levels reduced intestinal malondialdehyde contents (linear and quadratic, P < 0.05) and jejunal total superoxide dismutase (T-SOD) activity (linear, P < 0.05), and enhanced (linear and quadratic, P<0.05) ileal catalase and T-SOD activities in squabs, and these effects were more prominent in the 17% CP diet group. Graded CP levels up-regulated the mRNA expression of intestinal zonula occludens 1 (linear, P < 0.05), solute carrier family 7 members 9 (linear, P < 0.05) and claudin 1 (CLDN1, linear and quadratic, P < 0.05), ileal CLDN3 and solute carrier family 6 members 14 (linear, P < 0.05) but lowered jejunal solute carrier family 6 member 14 (quadratic, P<0.05) mRNA expression in squabs. The effects of dietary CP levels on intestinal tight junction proteins expression were more apparent when its supplemental levels were 18%. These results suggested that increasing parental dietary CP levels ranged from 14 to 18% during breeding period improved growth and intestinal function of squabs, with its recommended level being 17%.

2.
Environ Sci Pollut Res Int ; 31(24): 35332-35352, 2024 May.
Artigo em Inglês | MEDLINE | ID: mdl-38727971

RESUMO

Petroleum hydrocarbons are a stubborn pollutant that is difficult to degrade globally, and plant-microbial degradation is the main way to solve this type of pollutant. In this study, the physiological and ecological responses of alfalfa to petroleum hydrocarbons in different concentrations of petroleum hydrocarbon-contaminated soil with KB1 (Rhodococcus erythropolis) were analyzed and determined by laboratory potting techniques. The growth of alfalfa (CK) and alfalfa with KB1 (JZ) in different concentrations of petroleum hydrocarbons contaminated soil was compared and analyzed. The results of the CK group showed that petroleum hydrocarbons could significantly affect the activity of alfalfa antioxidant enzyme system, inhibit the development of alfalfa roots and the normal growth of plants, especially in the high-concentration group. KB1 strain had the ability to produce IAA, form biofilm, fix nitrogen, produce betaine and ACC deaminase, and the addition of KB1 could improve the growth traits of alfalfa in the soil contaminated with different concentrations of petroleum hydrocarbons, the content of soluble sugars in roots, and the stress resistance and antioxidant enzyme activities of alfalfa. In addition, the degradation kinetics of the strain showed that the degradation rate of petroleum could reach 75.2% after soaking with KB1. Furthermore, KB1 can efficiently degrade petroleum hydrocarbons in advance and significantly alleviate the damage of high concentration of petroleum hydrocarbons to plant roots. The results showed that KB1 strains and alfalfa plants could effectively enhance the degradation of petroleum hydrocarbons, which provided new ideas for improving bioremediation strategies.


Assuntos
Biodegradação Ambiental , Hidrocarbonetos , Medicago sativa , Petróleo , Rhodococcus , Poluentes do Solo , Petróleo/metabolismo , Poluentes do Solo/metabolismo , Rhodococcus/metabolismo , Hidrocarbonetos/metabolismo , Microbiologia do Solo , Raízes de Plantas/metabolismo
3.
Microb Cell Fact ; 23(1): 155, 2024 May 27.
Artigo em Inglês | MEDLINE | ID: mdl-38802857

RESUMO

BACKGROUND: Rhizomucor miehei (RM) lipase is a regioselective lipase widely used in food, pharmaceutical and biofuel industries. However, the high cost and low purity of the commercial RM lipase limit its industrial applications. Therefore, it is necessary to develop cost-effective strategies for large-scale preparation of this lipase. The present study explored the high-level expression of RM lipase using superfolder green fluorescent protein (sfGFP)-mediated Escherichia coli secretion system. RESULTS: The sfGFP(-15) mutant was fused to the C-terminus of RM lipase to mediate its secretion expression. The yield of the fusion protein reached approximately 5.1 g/L with high-density fermentation in 5-L fermentors. Unlike conventional secretion expression methods, only a small portion of the target protein was secreted into the cell culture while majority of the fusion protein was still remained in the cytoplasm. However, in contrast to intracellular expression, the target protein in the cytoplasm could be transported efficiently to the supernatant through a simple washing step with equal volume of phosphate saline (PBS), without causing cell disruption. Hence, the approach facilitated the downstream purification step of the recombinant RM lipase. Moreover, contamination or decline of the engineered strain and degradation or deactivation of the target enzyme can be detected efficiently because they exhibited bright green fluorescence. Next, the target protein was immobilized with anion-exchange and macropore resins. Diethylaminoethyl sepharose (DEAE), a weak-basic anion-exchange resin, exhibited the highest bind capacity but inhibited the activity of RM lipase dramatically. On the contrary, RM lipase fixed with macropore resin D101 demonstrated the highest specific activity. Although immobilization with D101 didn't improve the activity of the enzyme, the thermostability of the immobilized enzyme elevated significantly. The immobilized RM lipase retained approximately 90% of its activity after 3-h incubation at 80 °C. Therefore, D101 was chosen as the supporting material of the target protein. CONCLUSION: The present study established a highly efficient strategy for large-scale preparation of RM lipase. This innovative technique not only provides high-purity RM lipase at a low cost but also has great potential as a platform for the preparation of lipases in the future.


Assuntos
Escherichia coli , Lipase , Rhizomucor , Lipase/genética , Lipase/metabolismo , Lipase/química , Rhizomucor/enzimologia , Rhizomucor/genética , Escherichia coli/genética , Escherichia coli/metabolismo , Enzimas Imobilizadas/metabolismo , Enzimas Imobilizadas/genética , Enzimas Imobilizadas/química , Proteínas de Fluorescência Verde/metabolismo , Proteínas de Fluorescência Verde/genética , Proteínas Recombinantes de Fusão/genética , Proteínas Recombinantes de Fusão/metabolismo , Proteínas Recombinantes de Fusão/química , Proteínas Recombinantes de Fusão/biossíntese , Fermentação
4.
Food Chem Toxicol ; 189: 114746, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38768936

RESUMO

Diesel exhaust particle (DEP) exposure induces a variety of toxicological effects through oxidative stress and inflammation responses. This research investigated the mechanisms underlying DEP-induced GC-1spg cells oxidative stress by examining ROS accumulation, antioxidant defense systems activation, mitochondrial dysfunction, and the Nrf2/Keap1/HO-1 pathway response. Subsequently, we further evaluated the ATP levels, ATP5α synthase activity and ATP5α synthase S-sulfhydrated modification in DEP-exposed GC-1 spg cells. The results showed that DEP exposure significantly inhibited cell proliferation and viability, increased intracellular ROS production, decreased MMP, down-regulated antioxidant capacity, activated the Nrf2/Keap1/HO-1 pathway. However, DEP-induced oxidative stress was partially alleviated by GSH and exogenous H2S. In addition, DEP exposure induced ATP depletion and ATP5α synthase inactivity in GC-1 spg cells, accompanied by ATP5α synthase S-sulfhydrated modification. In conclusion, our research showed that DEP may incapacitate mitochondria through oxidative stress injury, leading to GC-1 spg cells oxidative stress. This process may be associated with the reduction of ATP5α1 S-sulfhydrated modification. It provides a new perspective for the research of the mechanism related to male reproductive toxicity due to air pollution.


Assuntos
Proteína 1 Associada a ECH Semelhante a Kelch , Fator 2 Relacionado a NF-E2 , Estresse Oxidativo , Material Particulado , Emissões de Veículos , Estresse Oxidativo/efeitos dos fármacos , Emissões de Veículos/toxicidade , Animais , Proteína 1 Associada a ECH Semelhante a Kelch/metabolismo , Fator 2 Relacionado a NF-E2/metabolismo , Camundongos , Material Particulado/toxicidade , ATPases Mitocondriais Próton-Translocadoras/metabolismo , Espécies Reativas de Oxigênio/metabolismo , Transdução de Sinais/efeitos dos fármacos , Linhagem Celular , Mitocôndrias/efeitos dos fármacos , Mitocôndrias/metabolismo , Sobrevivência Celular/efeitos dos fármacos , Trifosfato de Adenosina/metabolismo , Proliferação de Células/efeitos dos fármacos
5.
Animals (Basel) ; 14(7)2024 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-38612286

RESUMO

The Taihu Dianzi pigeon is a breed native to China, and its special piebalding, crest, and polydactyly phenotypes are the result of artificial and natural selection. Here, we analyzed the genetic differences among three kinds of pigeons with different phenotypes at the genomic level. A selective sweep was conducted based on the fixation index (FST) and nucleotide diversity (π) ratio, and the results revealed that MC1R was related to the formation of the distinctive piebalding of the Taihu Dianzi pigeon. Combined with the results of genome-wide association studies, we identified candidate genes associated with the crest (SMYD and STOX2) and polydactyly (SLC52A3 and ANGPT4). The candidate genes identified in this study and their variants may be useful for understanding the genetic mechanism underlying the special phenotypes of the Taihu Dianzi pigeon. This study provides new insights into the genetic factors that may influence the formation of the special piebalding, crest, and polydactyly characteristics in pigeons.

6.
Methods ; 222: 112-121, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-38215898

RESUMO

Design of molecules for candidate compound selection is one of the central challenges in drug discovery due to the complexity of chemical space and requirement of multi-parameter optimization. Here we present an application scenario-oriented platform (ID4Idea) for molecule generation in different scenarios of drug discovery. This platform utilizes both library or rule based and generative based algorithms (VAE, RNN, GAN, etc.), in combination with various AI learning types (pre-training, transfer learning, reinforcement learning, active learning, etc.) and input representations (1D SMILES, 2D graph, 3D shape, binding site, pharmacophore, etc.), to enable customized solutions for a given molecular design scenario. Besides the usual generation followed screening protocol, goal-directed molecule generation can also be conducted towards predefined goals, enhancing the efficiency of hit identification, lead finding, and lead optimization. We demonstrate the effectiveness of ID4Idea platform through case studies, showcasing customized solutions for different design tasks using various input information, such as binding pockets, pharmacophores, and compound representations. In addition, remaining challenges are discussed to unlock the full potential of AI models in drug discovery and pave the way for the development of novel therapeutics.


Assuntos
Desenho de Fármacos , Descoberta de Drogas , Sítios de Ligação , Algoritmos , Biblioteca Gênica
7.
Curr Pharm Biotechnol ; 25(4): 396-410, 2024.
Artigo em Inglês | MEDLINE | ID: mdl-37612860

RESUMO

Ferroptosis is an iron-dependent programmed cell death mode that is distinct from other cell death modes, and radiation is able to stimulate cellular oxidative stress and induce the production of large amounts of reactive oxygen radicals, which in turn leads to the accumulation of lipid peroxide and the onset of ferroptosis. In this review, from the perspective of the role of ferroptosis in generating a radiation response following cellular irradiation, the relationship between ferroptosis induced by ionizing radiation stress and the response to ionizing radiation is reviewed, including the roles of MAPK and Nrf2 signaling pathways in ferroptosis, resulting from the oxidative stress response to ionizing radiation, the metabolic regulatory role of the p53 gene in ferroptosis, and regulatory modes of action of iron metabolism and iron metabolism-related regulatory proteins in promoting and inhibiting ferroptosis. It provides some ideas for the follow-up research to explore the specific mechanism and regulatory network of ferroptosis in response to ionizing radiation.


Assuntos
Ferroptose , Morte Celular , Peróxidos Lipídicos , Radiação Ionizante , Espécies Reativas de Oxigênio , Ferro
8.
J Chem Theory Comput ; 20(2): 799-818, 2024 Jan 23.
Artigo em Inglês | MEDLINE | ID: mdl-38157475

RESUMO

Biomolecular simulations have become an essential tool in contemporary drug discovery, and molecular mechanics force fields (FFs) constitute its cornerstone. Developing a high quality and broad coverage general FF is a significant undertaking that requires substantial expert knowledge and computing resources, which is beyond the scope of general practitioners. Existing FFs originate from only a limited number of groups and organizations, and they either suffer from limited numbers of training sets, lower than desired quality because of oversimplified representations, or are costly for the molecular modeling community to access. To address these issues, in this work, we developed an AMBER-consistent small molecule FF with extensive chemical space coverage, and we provide Open Access parameters for the entire modeling community. To validate our FF, we carried out benchmarks of quantum mechanics (QM)/molecular mechanics conformer comparison and free energy perturbation calculations on several benchmark data sets. Our FF achieves a higher level of performance at reproducing QM energies and geometries than two popular open-source FFs, OpenFF2 and GAFF2. In relative binding free energy calculations for 31 protein-ligand data sets, comprising 1079 pairs of ligands, the new FF achieves an overall root-mean-square error of 1.19 kcal/mol for ΔΔG and 0.92 kcal/mol for ΔG on a subset of 463 ligands without bespoke fitting to the data sets. The results are on par with those of the leading commercial series of OPLS FFs.


Assuntos
Benchmarking , Simulação de Dinâmica Molecular , Termodinâmica , Entropia , Proteínas/química , Ligantes
9.
J Chem Phys ; 159(24)2023 Dec 28.
Artigo em Inglês | MEDLINE | ID: mdl-38153154

RESUMO

Natural gas hydrates, mainly existing in permafrost and on the seabed, are expected to be a new energy source with great potential. The exploitation technology of natural gas hydrates is one of the main focuses of hydrate-related studies. In this study, a large-size liquid aqueous solution wrapping a methane hydrate system was established and molecular dynamics simulations were used to investigate the phase equilibrium conditions of methane hydrate at different methane concentrations and interfacial geometries. It is found that the methane concentration of a solution significantly affects the phase equilibrium of methane hydrates. Different methane concentrations at the same temperature and pressure can lead to hydrate formation or decomposition. At the same temperature and pressure, in a system reaching equilibrium, the size of spherical hydrate clusters is coupled to the solution concentration, which is proportional to the Laplace pressure at the solid-liquid interface. Lower solution concentrations reduce the phase equilibrium temperature of methane hydrates at the same pressure; as the concentration increases, the phase equilibrium temperature gradually approaches the actual phase equilibrium temperature. In addition, the interfacial geometry of hydrates affects the thermodynamic stability of hydrates. The spherical hydrate particles have the highest stability for the same volume. Through this study, we provide a stronger foundation to understand the principles driving hydrate formation/dissociation relevant to the exploitation of methane hydrates.

10.
J Phys Chem B ; 127(48): 10447-10457, 2023 Dec 07.
Artigo em Inglês | MEDLINE | ID: mdl-37991934

RESUMO

Electric fields have been proven to be capable of significantly affecting the equilibrium state of hydrates. In this study, the thermodynamic properties and structural changes of methane hydrate (MH) in various anion solutions in an electric field at 0.7 V/nm were investigated by molecular dynamics simulations. The presence of anions significantly enhances the instability of methane hydrates under electric fields, leading to a staged dissociation process. First, the anions coexist with MH to form a temporary metastable structure under the action of an electric field. Then, the migration of anions causes the dissociation of nearby hydrates and the formation of flow channels in the hydrate layer, which leads to the complete dissociation of MH after a period. The promotive effects of F-, Br-, I-, and Cl- ions were close, while SO42- was relatively weak. The anions are still in hydration shells in the MH phase, but the structure of the hydration shells differs slightly from that in solution (the coordination numbers of I- and SO42- ions increased). The migration resistances of multiple anions to cross the surface of the hydrate layer are similar. However, inside the hydrate phase, the anions with a larger radius have a higher migration resistance. It is difficult for SO42- ions to migrate inside the hydrate phase, and they tend to form a metastable structure on the hydrate surface. Combining our previous studies, SrCl2 solution has the best hydrate promotion under an electric field environment.

11.
J Fungi (Basel) ; 9(10)2023 Oct 16.
Artigo em Inglês | MEDLINE | ID: mdl-37888278

RESUMO

Paraphoma chrysanthemicola is a newly identified endophytic fungus. The focus of most studies on P. chrysanthemicola has been on its isolation, identification and effects on plants. However, the limited genomic information is a barrier to further research. Therefore, in addition to studying the morphological and physiological characteristics of P. chrysanthemicola, we sequenced its genome and compared it with that of Paraphoma sp. The results showed that sucrose, peptone and calcium phosphate were suitable sources of carbon, nitrogen and phosphorus for this strain. The activities of amylase, cellulase, chitosanase, lipase and alkaline protease were also detected. Sequencing analysis revealed that the genome of P. chrysanthemicola was 44.1 Mb, with a scaffold N50 of 36.1 Mb and 37,077 protein-coding genes. Gene Ontology (GO) annotation showed that mannose-modified glycosylation was predominant in monosaccharide utilisation. The percentage of glycoside hydrolase (GH) modules was the highest in the carbohydrate-active enzymes database (CAZy) analysis. Secondary metabolite-associated gene cluster analysis identified melanin, dimethylcoprogen and phyllostictine A biosynthetic gene clusters (>60% similarity). The results indicated that P. chrysanthemicola had a mannose preference in monosaccharide utilisation and that melanin, dimethylcoprogen and phyllostictine A were important secondary metabolites for P. chrysanthemicola as an endophytic fungus.

12.
Sci Rep ; 13(1): 17434, 2023 10 13.
Artigo em Inglês | MEDLINE | ID: mdl-37833424

RESUMO

Lung adenocarcinoma (LUAD) remains a leading cause of cancer-related morbidity and mortality globally. While DDX52, an ATP-dependent RNA helicase, plays a role in several biological processes, its specific involvement in LUAD is yet to be elucidated. We utilized ROC curves to determine DDX52's predictive potential for LUAD. Kaplan-Meier survival curves, along with univariate and multivariate Cox analyses, assessed the prognostic implications of DDX52 in LUAD. We constructed nomogram models to further delineate DDX52's influence on prognosis, employed GSEA for functional analysis, and used qRT-PCR to examine DDX52 expression in LUAD tissues. DDX52 expression was notably higher in LUAD tissues, suggesting its potential as a negative prognostic marker. We observed a direct relationship between DDX52 expression and advanced T and N stages, as well as higher grading and staging in LUAD patients. Cox analyses further underscored DDX52's role as an independent prognostic determinant for LUAD. GSEA insights indicated DDX52's influence on LUAD progression via multiple signaling pathways. Our nomogram, founded on DDX52 expression, effectively projected LUAD patient survival, as validated by calibration curves. Elevated DDX52 expression in LUAD tissues signals its potential as a poor prognostic marker. Our findings emphasize DDX52's role not only as an independent prognostic factor for LUAD but also as a significant influencer in its progression through diverse signaling pathways. The constructed nomogram also underscores the feasibility of predicting LUAD patient survival based on DDX52 expression.


Assuntos
Adenocarcinoma de Pulmão , Adenocarcinoma , Neoplasias Pulmonares , Humanos , Prognóstico , RNA Helicases , DNA Helicases , Expressão Gênica , Biomarcadores
13.
Materials (Basel) ; 16(16)2023 Aug 13.
Artigo em Inglês | MEDLINE | ID: mdl-37629898

RESUMO

Precipitate free zones (PFZs) near grain boundaries generally soften alloys. The quenching rate after solution treatment is an important factor influencing the width of PFZs in Al-Mg-Si-Cu alloy. This study explored the effects of high quenching rates on the grain boundary microstructures and mechanical properties of an Al-Mg-Si-Cu alloy. Samples of various thickness were quenched in water at room temperature and in ethylene glycol at -40 °C, respectively. The results showed that the rapidly quenched samples at -40 °C exhibited better comprehensive mechanical properties than the water-quenched samples. Transmission electron microscopy studies revealed the rapidly quenched samples had wider PFZs, shorter intragranular precipitates, and larger grain boundary precipitates (GBPs) than water-quenched samples. It is proposed that when the quenching rate exceeds the critical cooling rate, e.g., in water quenching or rapid quenching, the formation of PFZs is controlled by the solute depletion mechanism rather than the vacancy depletion mechanism. The nucleation and growth of GBPs thus lead to the depletion of solute atoms, resulting in wider PFZs rather than thinner PFZs according to previous knowledge. This research provides valuable insights into the application of rapid quenching technology for modifying alloys' microstructures and properties.

14.
J Food Sci ; 88(10): 4275-4288, 2023 Oct.
Artigo em Inglês | MEDLINE | ID: mdl-37615996

RESUMO

The antitumor effects of a whey peptide-based enteral diet, whose main components are whey peptides and yogurt fermented by Lactobacillus delbureckii subsp. bulgaricus 2038 and Streptococcus thermophilus 1131, were investigated in mice. Our results indicated that the tumor weight in C26 carcinoma-transplanted mice was significantly smaller at day 16 post-implantation in the whey peptide-based enteral diet group (1.36 ± 0.54 g) than in the control group (1.83 ± 0.89 g) (p < 0.05). The whey peptide-based enteral diet group exhibited higher tumor cell apoptosis, lower cell proliferation, and inactive angiogenesis indicating by higher degree of TUNEL, lower positive rates of Ki-67, VEGF, and CD34 than control group. It also attenuated inflammatory cell infiltration of spleen and liver as indicated by the decreased spleen index (10.89 ± 2.06 vs. 12.85 ± 2.92, p < 0.05) and increased liver index (58.09 ± 11.37 vs. 53.19 ± 6.67, p < 0.05) in the whey peptide-based enteral diet group than the control diet group. These results proved the inhibitory effect of the whey peptide-based enteral diet on tumor growth, which might be attributed to the whey peptides component. PRACTICAL APPLICATION: A whey peptide-based enteral diet (MEIN® ), containing cheese whey and multiple nutrients, was selected to verify the anti-tumor effect by animal experiments. The tumor weight growth, tumor cell proliferation, inflammatory cell infiltration of spleen and liver in tumor model mice was significantly attenuated by the whey peptide-based enteral diet, that might be attributed to its whey peptides component. These results provided an additive direction for cancer therapy and need a further study including clinical trials.

15.
Open Med (Wars) ; 18(1): 20230754, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37533740

RESUMO

Irreversible cardiomyopathy was caused by the therapeutic of anthracyclines in the chemotherapy of cancers. The cell apoptosis and autophagy were induced by anthracyclines in AC16 cells. MiR-223-3p ascends in anthracycline-treated AC16, but the expression of nuclear factor I-A (NFIA) was specifically down-regulated. However, the underlying molecular mechanism between NFIA and miR-223-3p is unclear now in AC16 cells. In our research, NFIA expression was dampened in AC16 cells by miR-223-3p mimics. Additionally, miR-223-3p knockdown hindered the apoptosis and autophagy in anthracycline-treated AC16. Furthermore, NFIA was predicted and verified as a miR-223-3p's downstream target and rescued the functions of miR-223-3p. These findings illustrated that miR-223-3p advances anthracycline-stimulated cardiomyocyte damage progression by targeting NFIA, implying the promising therapeutic function of miR-223-3p on cardiomyocyte damage in cancer patients.

16.
J Chem Inf Model ; 63(16): 5341-5355, 2023 08 28.
Artigo em Inglês | MEDLINE | ID: mdl-37549337

RESUMO

Computer-aided drug design (CADD), especially artificial intelligence-driven drug design (AIDD), is increasingly used in drug discovery. In this paper, a novel and efficient workflow for hit identification was developed within the ID4Inno drug discovery platform, featuring innovative artificial intelligence, high-accuracy computational chemistry, and high-performance cloud computing. The workflow was validated by discovering a few potent hit compounds (best IC50 is ∼0.80 µM) against PI5P4K-ß, a novel anti-cancer target. Furthermore, by applying the tools implemented in ID4Inno, we managed to optimize these hit compounds and finally obtained five hit series with different scaffolds, all of which showed high activity against PI5P4K-ß. These results demonstrate the effectiveness of ID4inno in driving hit identification based on artificial intelligence, computational chemistry, and cloud computing.


Assuntos
Inteligência Artificial , Química Computacional , Desenho de Fármacos , Descoberta de Drogas/métodos
17.
PLoS Comput Biol ; 19(7): e1011222, 2023 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-37410793

RESUMO

The COVID-19 pandemic caused by the SARS-CoV-2 virus has resulted in millions of deaths worldwide. The disease presents with various manifestations that can vary in severity and long-term outcomes. Previous efforts have contributed to the development of effective strategies for treatment and prevention by uncovering the mechanism of viral infection. We now know all the direct protein-protein interactions that occur during the lifecycle of SARS-CoV-2 infection, but it is critical to move beyond these known interactions to a comprehensive understanding of the "full interactome" of SARS-CoV-2 infection, which incorporates human microRNAs (miRNAs), additional human protein-coding genes, and exogenous microbes. Potentially, this will help in developing new drugs to treat COVID-19, differentiating the nuances of long COVID, and identifying histopathological signatures in SARS-CoV-2-infected organs. To construct the full interactome, we developed a statistical modeling approach called MLCrosstalk (multiple-layer crosstalk) based on latent Dirichlet allocation. MLCrosstalk integrates data from multiple sources, including microbes, human protein-coding genes, miRNAs, and human protein-protein interactions. It constructs "topics" that group SARS-CoV-2 with genes and microbes based on similar patterns of co-occurrence across patient samples. We use these topics to infer linkages between SARS-CoV-2 and protein-coding genes, miRNAs, and microbes. We then refine these initial linkages using network propagation to contextualize them within a larger framework of network and pathway structures. Using MLCrosstalk, we identified genes in the IL1-processing and VEGFA-VEGFR2 pathways that are linked to SARS-CoV-2. We also found that Rothia mucilaginosa and Prevotella melaninogenica are positively and negatively correlated with SARS-CoV-2 abundance, a finding corroborated by analysis of single-cell sequencing data.


Assuntos
COVID-19 , MicroRNAs , Humanos , SARS-CoV-2/genética , Síndrome de COVID-19 Pós-Aguda , Pandemias/prevenção & controle , MicroRNAs/genética
18.
Sci Prog ; 106(2): 368504231181769, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37306208

RESUMO

Cyclone separation is an effective method for the treatment of oily wastewater from offshore oil production platforms. There is a lack of research on the impact of dispersion on the separation efficiency of current liquid-liquid separation hydrocyclones. A numerical simulation method was used to study the effect of the oil droplet characteristic parameters on the separation efficiency of a hydrocyclone oil removal device. An analysis of the trajectory of oil droplets revealed the oil removal mechanism of the hydrocyclone oil removal device: under the guidance of tangential velocity, the oil-water mixed fluid in the equipment generates different centrifugal forces due to the density difference, so oil and water adopt different flow paths to flow out. The effects of the particle diameter, velocity, and concentration of the inlet oil droplet on the separation efficiency were investigated. The droplet size had a positive effect on the separation efficiency, the oil concentration had a negative effect on the separation efficiency, and the speed of the oil drop was directly proportional to the separation efficiency within a certain range. These studies improved the basis for the efficient application of hydrocyclone oil removal devices.

19.
Genes (Basel) ; 14(6)2023 05 24.
Artigo em Inglês | MEDLINE | ID: mdl-37372316

RESUMO

Jujubosides are the major medicinal ingredients of Ziziphi Spinosae Semen (the seed of wild jujube). To date, a complete understanding of jujuboside's metabolic pathways has not been attained. This study has systematically identified 35 ß-glucosidase genes belonging to the glycoside hydrolase family 1 (GH1) using bioinformatic methods based on the wild jujube genome. The conserved domains and motifs of the 35 putative ß-glucosidases, along with the genome locations and exon-intron structures of 35 ß-glucosidase genes were revealed. The potential functions of the putative proteins encoded by the 35 ß-glucosidase genes are suggested based on their phylogenetic relationships with Arabidopsis homologs. Two wild jujube ß-glucosidase genes were heterologously expressed in Escherichia coli, and the recombinant proteins were able to convert jujuboside A (JuA) into jujuboside B (JuB). Since it has been previously reported that JuA catabolites, including JuB and other rare jujubosides, may play crucial roles in the jujuboside's pharmacological activity, it is suggested that these two proteins can be used to enhance the utilization potential of jujubosides. This study provides new insight into the metabolism of jujubosides in wild jujube. Furthermore, the characterization of ß-glucosidase genes is expected to facilitate investigations involving the cultivation and breeding of wild jujube.


Assuntos
Arabidopsis , Ziziphus , Glicosídeo Hidrolases/genética , Ziziphus/genética , beta-Glucosidase/genética , Filogenia , Melhoramento Vegetal
20.
Curr Top Med Chem ; 23(19): 1835-1849, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37151173

RESUMO

Titanocene dichloride and budotitane have opened a new chapter in medicinal chemistry of titanium(IV) complexes being novel non-platinum antitumor metallic agents. Numerous efforts have led to the discovery of the diamino bis-phenolato titanium(IV) complexes. Among which, the [ONNO] and [ONON] type ligands namely Salan, Salen and Salalen coordinated titanium(IV) alkoxyl complexes have demonstrated significantly enhanced aqueous stability, their in vitro and in vivo antitumor efficacy, mechanism of action, structure-activity relationships and combined tumor therapy have been intensively investigated. Replacement of the labile alkoxyls with a second chelator resulted in structural rigid titanium(IV) complexes, which showed exceedingly good aqueous stability and potent antitumor activity both in vitro and in vivo. The unique ligand system successfully allowed the access of isotopic [45Ti]Titanium(IV) complexes, post-synthetic modification, facile synthetic protocols and antitumor congeneric zirconium(IV) and hafnium(IV) complexes. This review presents recent research progress in the field of antitumor group 4 metal complexes stabilized with phenolato ligands; especially their structure-activity relationships are summarized.


Assuntos
Antineoplásicos , Complexos de Coordenação , Neoplasias , Compostos Organometálicos , Humanos , Titânio/farmacologia , Titânio/química , Titânio/uso terapêutico , Ligantes , Neoplasias/tratamento farmacológico , Compostos Organometálicos/química , Compostos Organometálicos/farmacologia , Compostos Organometálicos/uso terapêutico , Relação Estrutura-Atividade , Antineoplásicos/química , Complexos de Coordenação/farmacologia
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