In this paper we investigate the influence of cold plasma as novel method on the external otitis treatment which is a frequent cause of earache. 24 infected external auditory canals in 24 rats were categorized in four experimental groups including control, plasma exposed, ciprofloxacin drug and mixed of plasma-ciprofloxacin groups. In plasma group, dielectric barrier discharge was employed as the source of cold plasma in 5 days. All rats were observed with otoscope daily and a scoring system was used to evaluate swelling and effusion of the ear canal. Number of colonies in microbiological culture were counted in each group during the first 5 days after treatment. For the multiple group comparisons of swelling and effusion measured in the external auditory canal, Kruskal–Wallis analysis was applied and one-way anova and Kruskal–Wallis analysis was used for the statistical analysis of the results of the cultures in different days. Also, Tukey and Mann–Whitney tests was applied for multiple comparisons. Our findings show that swelling and effusion were obviously reduced in plasma group compared to control group (P < 0.01). Number of colonies in control group was statistically different from those in drug, plasma, and mixed group on the second to fifth day (p < 0.001). According to the results cold plasma can be introduced as an impressive method for external otitis treatment. Moreover, when cold plasma joined to antibiotic method, it leads to a superior performance respecting plasma or antibiotic method alone.
{"title":"The effect of cold plasma on the treatment of external otitis: an experimental study in rats","authors":"Tayebe Taghizade, Alireza Akbarzadeh-Baghban, Nasrin Navab Safa","doi":"10.1186/s13568-024-01748-7","DOIUrl":"https://doi.org/10.1186/s13568-024-01748-7","url":null,"abstract":"<p>In this paper we investigate the influence of cold plasma as novel method on the external otitis treatment which is a frequent cause of earache. 24 infected external auditory canals in 24 rats were categorized in four experimental groups including control, plasma exposed, ciprofloxacin drug and mixed of plasma-ciprofloxacin groups. In plasma group, dielectric barrier discharge was employed as the source of cold plasma in 5 days. All rats were observed with otoscope daily and a scoring system was used to evaluate swelling and effusion of the ear canal. Number of colonies in microbiological culture were counted in each group during the first 5 days after treatment. For the multiple group comparisons of swelling and effusion measured in the external auditory canal, Kruskal–Wallis analysis was applied and one-way anova and Kruskal–Wallis analysis was used for the statistical analysis of the results of the cultures in different days. Also, Tukey and Mann–Whitney tests was applied for multiple comparisons. Our findings show that swelling and effusion were obviously reduced in plasma group compared to control group (<i>P</i> < 0.01). Number of colonies in control group was statistically different from those in drug, plasma, and mixed group on the second to fifth day (<i>p</i> < 0.001). According to the results cold plasma can be introduced as an impressive method for external otitis treatment. Moreover, when cold plasma joined to antibiotic method, it leads to a superior performance respecting plasma or antibiotic method alone.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219539","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1186/s13568-024-01756-7
Yan Yan, Haisheng Yuan, Fan Yang, Heiya Na, Xiuling Yu, Jingran Liu, Yuzhen Wang
Non-alcoholic fatty liver disease (NAFLD) is becoming a significant global public health threat. Seabuckthorn (Hippophae rhamnoides L.) has been used in traditional Chinese medicine (TCM). The hypolipidemic effects of Seabuckthorn polysaccharides (SP) against high-fat diets (HFD)-induced NAFLD were systematically explored and compared with that of Bifidobacterium lactis V9 (B. Lactis V9). Results showed that HFD-induced alanine transaminase (ALT) and aspartate aminotransferase (AST) levels decreased by 2.8-fold and 4.5-fold, respectively, after SP supplementation. Moreover, the alleviating effect on hepatic lipid accumulation is better than that of B. Lactis V9. The ACC and FASN mRNA levels were significantly reduced by 1.8 fold (P < 0.05) and 2.3 folds (P < 0.05), respectively, while the CPT1α and PPARα mRNA levels was significantly increased by 2.3 fold (P < 0.05) and 1.6 fold (P < 0.05), respectively, after SP administration. SP activated phosphorylated-AMPK and inhibited PPARγ protein expression, improved serum oxidative stress and inflammation (P < 0.05). SP supplementation leads to increased hepatic expression of nuclear factor erythroid 2-related factor 2 (Nrf-2), heme oxygenase-1 (HO-1) and Superoxide dismutase-2 (SOD-2). Furthermore, SP treatment improved HFD-induced intestinal dysbiosis. Lentisphaerae, Firmicutes, Tenericutes and Peptococcus sp., RC9_gut_group sp., and Parabacteroides sp. of the gut microbiota were significantly associated with hepatic steatosis and indicators related to oxidative stress and inflammation. Therefore, SP can mitigate hepatic lipid accumulation by regulating Nrf-2/HO-1 signaling pathways and gut microbiota. This study offers new evidence supporting the use of SP as a prebiotic treatment for NAFLD.
{"title":"Seabuckthorn polysaccharides mitigate hepatic steatosis by modulating the Nrf-2/HO-1 pathway and gut microbiota","authors":"Yan Yan, Haisheng Yuan, Fan Yang, Heiya Na, Xiuling Yu, Jingran Liu, Yuzhen Wang","doi":"10.1186/s13568-024-01756-7","DOIUrl":"https://doi.org/10.1186/s13568-024-01756-7","url":null,"abstract":"<p>Non-alcoholic fatty liver disease (NAFLD) is becoming a significant global public health threat. Seabuckthorn (<i>Hippophae rhamnoides</i> L.) has been used in traditional Chinese medicine (TCM). The hypolipidemic effects of Seabuckthorn polysaccharides (SP) against high-fat diets (HFD)-induced NAFLD were systematically explored and compared with that of <i>Bifidobacterium lactis</i> V9 (<i>B. Lactis</i> V9). Results showed that HFD-induced alanine transaminase (ALT) and aspartate aminotransferase (AST) levels decreased by 2.8-fold and 4.5-fold, respectively, after SP supplementation. Moreover, the alleviating effect on hepatic lipid accumulation is better than that of <i>B. Lactis</i> V9. The ACC and FASN mRNA levels were significantly reduced by 1.8 fold (<i>P</i> < 0.05) and 2.3 folds (<i>P</i> < 0.05), respectively, while the CPT1α and PPARα mRNA levels was significantly increased by 2.3 fold (<i>P</i> < 0.05) and 1.6 fold (<i>P</i> < 0.05), respectively, after SP administration. SP activated phosphorylated-AMPK and inhibited PPARγ protein expression, improved serum oxidative stress and inflammation (<i>P</i> < 0.05). SP supplementation leads to increased hepatic expression of nuclear factor erythroid 2-related factor 2 (Nrf-2), heme oxygenase-1 (HO-1) and Superoxide dismutase-2 (SOD-2). Furthermore, SP treatment improved HFD-induced intestinal dysbiosis. <i>Lentisphaerae</i>,<i> Firmicutes</i>,<i> Tenericutes</i> and <i>Peptococcus </i>sp.,<i> RC9_gut_group </i>sp., and <i>Parabacteroides </i>sp. of the gut microbiota were significantly associated with hepatic steatosis and indicators related to oxidative stress and inflammation. Therefore, SP can mitigate hepatic lipid accumulation by regulating Nrf-2/HO-1 signaling pathways and gut microbiota. This study offers new evidence supporting the use of SP as a prebiotic treatment for NAFLD.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142219540","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-09DOI: 10.1186/s13568-024-01762-9
Muhammad Umer Khan, Azra Sakhawat, Raima Rehman, Abbas Haider Wali, Muhammad Usman Ghani, Areeba Akram, Muhammad Arshad Javed, Qurban Ali, Zhou Yu-Ming, Daoud Ali, Zhou Yu-Ming
Cystic fibrosis transmembrane conductance regulator (CFTR) protein is an ion channel found in numerous epithelia and controls the flow of water and salt across the epithelium. The aim of our study to find natural compounds that can improve lung function for people with cystic fibrosis (CF) caused by the p.Gly628Arg (rs397508316) mutation of CFTR protein. The sequence of CFTR protein as a target structure was retrieved from UniProt and PDB database. The ligands that included Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and one Trikafta (R*) reference drug were screened out from PubChem database. Autodock vina software carried out docking, and binding energies between the drug and the target were included using docking-score. The following tools examined binding energy, interaction, stability, toxicity, and visualize protein-ligand complexes. The compounds having binding energies of -6.4, -5.1, -6.6, -5.1, and - 6.5 kcal/mol for Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and R*-drug, respectively with mutated CFTR (Gly628Arg) structure were chosen as the most promising ligands. The ligands bind to the mutated CFTR protein structure active sites in hydrophobic bonds, hydrogen bonds, and electrostatic interactions. According to ADMET analyses, the ligands Armepavine and Quercetin also displayed good pharmacokinetic and toxicity characteristics. An MD simulation for 200 ns was also established to ensure that Armepavine and Quercetin ligands attached to the target protein favorably and dynamically, and that protein-ligand complex stability was maintained. It is concluded that Armepavine and Quercetin have stronger capacity to inhibit the effect of mutated CFTR protein through improved trafficking and restoration of original function.
{"title":"Identification of novel natural compounds against CFTR p.Gly628Arg pathogenic variant.","authors":"Muhammad Umer Khan, Azra Sakhawat, Raima Rehman, Abbas Haider Wali, Muhammad Usman Ghani, Areeba Akram, Muhammad Arshad Javed, Qurban Ali, Zhou Yu-Ming, Daoud Ali, Zhou Yu-Ming","doi":"10.1186/s13568-024-01762-9","DOIUrl":"https://doi.org/10.1186/s13568-024-01762-9","url":null,"abstract":"<p><p>Cystic fibrosis transmembrane conductance regulator (CFTR) protein is an ion channel found in numerous epithelia and controls the flow of water and salt across the epithelium. The aim of our study to find natural compounds that can improve lung function for people with cystic fibrosis (CF) caused by the p.Gly628Arg (rs397508316) mutation of CFTR protein. The sequence of CFTR protein as a target structure was retrieved from UniProt and PDB database. The ligands that included Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and one Trikafta (R*) reference drug were screened out from PubChem database. Autodock vina software carried out docking, and binding energies between the drug and the target were included using docking-score. The following tools examined binding energy, interaction, stability, toxicity, and visualize protein-ligand complexes. The compounds having binding energies of -6.4, -5.1, -6.6, -5.1, and - 6.5 kcal/mol for Armepavine, Osthole, Curcumin, Plumbagine, Quercetin, and R*-drug, respectively with mutated CFTR (Gly628Arg) structure were chosen as the most promising ligands. The ligands bind to the mutated CFTR protein structure active sites in hydrophobic bonds, hydrogen bonds, and electrostatic interactions. According to ADMET analyses, the ligands Armepavine and Quercetin also displayed good pharmacokinetic and toxicity characteristics. An MD simulation for 200 ns was also established to ensure that Armepavine and Quercetin ligands attached to the target protein favorably and dynamically, and that protein-ligand complex stability was maintained. It is concluded that Armepavine and Quercetin have stronger capacity to inhibit the effect of mutated CFTR protein through improved trafficking and restoration of original function.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142153006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-03DOI: 10.1186/s13568-024-01761-w
Alma Ofelia Reyna-Campos, Beatriz Ruiz-Villafan, Martha Lydia Macías-Rubalcava, Elizabeth Langley, Romina Rodríguez-Sanoja, Sergio Sánchez
Lasso peptides, ribosomally synthesized and post-translationally modified peptides, are primarily produced by bacteria and some archaea. Streptomyces lasso peptides have been known for their antimicrobial, anticancer, and antiviral properties. However, understanding their role in the morphology and production of secondary metabolites remains limited. We identified a previously unknown lasso peptide gene cluster in the genome of Streptomyces sp. L06. This gene cluster (LASS) produces two distinct lasso peptides, morphosin-1 and - 2. Notably, morphosin-2 is a member of a new subfamily of lasso peptides, with BGCs exhibiting a similar structure. When LASS was expressed in different Streptomyces hosts, it led to exciting phenotypic changes, including the absence of spores and damage in aerial mycelium development. In one of the hosts, LASS even triggered antibiotic formation. These findings open up a world of possibilities, suggesting the potential role of morphosins in shaping Streptomyces' morphological and biochemical development.
{"title":"Heterologous expression of lasso peptides with apparent participation in the morphological development in Streptomyces.","authors":"Alma Ofelia Reyna-Campos, Beatriz Ruiz-Villafan, Martha Lydia Macías-Rubalcava, Elizabeth Langley, Romina Rodríguez-Sanoja, Sergio Sánchez","doi":"10.1186/s13568-024-01761-w","DOIUrl":"10.1186/s13568-024-01761-w","url":null,"abstract":"<p><p>Lasso peptides, ribosomally synthesized and post-translationally modified peptides, are primarily produced by bacteria and some archaea. Streptomyces lasso peptides have been known for their antimicrobial, anticancer, and antiviral properties. However, understanding their role in the morphology and production of secondary metabolites remains limited. We identified a previously unknown lasso peptide gene cluster in the genome of Streptomyces sp. L06. This gene cluster (LASS) produces two distinct lasso peptides, morphosin-1 and - 2. Notably, morphosin-2 is a member of a new subfamily of lasso peptides, with BGCs exhibiting a similar structure. When LASS was expressed in different Streptomyces hosts, it led to exciting phenotypic changes, including the absence of spores and damage in aerial mycelium development. In one of the hosts, LASS even triggered antibiotic formation. These findings open up a world of possibilities, suggesting the potential role of morphosins in shaping Streptomyces' morphological and biochemical development.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11371967/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118793","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-09-03DOI: 10.1186/s13568-024-01752-x
Miriam A Fingerhut, Lea Henrich, Christiane Lauber, Niklas Broel, Parviz Ghezellou, Dominik Karrer, Bernhard Spengler, Kim Langfelder, Timo Stressler, Holger Zorn, Martin Gand
The GDS(L)-like lipase from the Basidiomycota Pleurotus sapidus (PSA_Lip) was heterologously expressed using Trichoderma reesei with an activity of 350 U L-1. The isoelectric point of 5.0 was determined by isoelectric focusing. The novel PSA_Lip showed only 23.8-25.1%, 25.5%, 26.6% and 28.4% identity to the previously characterized GDSL-like enzymes phospholipase, plant lipase, acetylcholinesterase and acetylxylan esterase, from the carbohydrate esterase family 16, respectively. Therefore, the enzyme was purified from the culture supernatant and the catalytic properties and the substrate specificity of the enzyme were investigated using different assays to reveal its potential function. While no phospholipase, acetylcholinesterase and acetylxylan esterase activities were detected, studies on the hydrolysis of ferulic acid methyl ester (~ 8.3%) and feruloylated carbohydrate 5-O-transferuloyl-arabino-furanose (~ 0.8%) showed low conversions of these substrates. By investigating the hydrolytic activity towards p-nitrophenyl-(pNP)-esters with various chain-lengths, the highest activity was determined for medium chain-length pNP-octanoate at 65 °C and a pH value of 8, while almost no activity was detected for pNP-hexanoate. The enzyme is highly stable when stored at pH 10 and 4 °C for at least 7 days. Moreover, using consensus sequence analysis and homology modeling, we could demonstrate that the PSA_Lip does not contain the usual SGNH residues in the actives site, which are usually present in GDS(L)-like enzymes.
{"title":"Characterization of a GDS(L)-like hydrolase from Pleurotus sapidus with an unusual SGNH motif.","authors":"Miriam A Fingerhut, Lea Henrich, Christiane Lauber, Niklas Broel, Parviz Ghezellou, Dominik Karrer, Bernhard Spengler, Kim Langfelder, Timo Stressler, Holger Zorn, Martin Gand","doi":"10.1186/s13568-024-01752-x","DOIUrl":"10.1186/s13568-024-01752-x","url":null,"abstract":"<p><p>The GDS(L)-like lipase from the Basidiomycota Pleurotus sapidus (PSA_Lip) was heterologously expressed using Trichoderma reesei with an activity of 350 U L<sup>-1</sup>. The isoelectric point of 5.0 was determined by isoelectric focusing. The novel PSA_Lip showed only 23.8-25.1%, 25.5%, 26.6% and 28.4% identity to the previously characterized GDSL-like enzymes phospholipase, plant lipase, acetylcholinesterase and acetylxylan esterase, from the carbohydrate esterase family 16, respectively. Therefore, the enzyme was purified from the culture supernatant and the catalytic properties and the substrate specificity of the enzyme were investigated using different assays to reveal its potential function. While no phospholipase, acetylcholinesterase and acetylxylan esterase activities were detected, studies on the hydrolysis of ferulic acid methyl ester (~ 8.3%) and feruloylated carbohydrate 5-O-transferuloyl-arabino-furanose (~ 0.8%) showed low conversions of these substrates. By investigating the hydrolytic activity towards p-nitrophenyl-(pNP)-esters with various chain-lengths, the highest activity was determined for medium chain-length pNP-octanoate at 65 °C and a pH value of 8, while almost no activity was detected for pNP-hexanoate. The enzyme is highly stable when stored at pH 10 and 4 °C for at least 7 days. Moreover, using consensus sequence analysis and homology modeling, we could demonstrate that the PSA_Lip does not contain the usual SGNH residues in the actives site, which are usually present in GDS(L)-like enzymes.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11372007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142118792","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-31DOI: 10.1186/s13568-024-01755-8
Masaki Ishii, Tsuyoshi Yamada, Shinya Ohata
Trichophyton rubrum is one of the most frequently isolated fungi in patients with dermatophytosis. Despite its clinical significance, the molecular mechanisms of drug resistance and pathogenicity of T. rubrum remain to be elucidated because of the lack of genetic tools, such as efficient gene targeting systems. In this study, we generated a T. rubrum strain that lacks the nonhomologous end-joining-related gene ku80 (Δku80) and then developed a highly efficient genetic recombination system with gene targeting efficiency that was 46 times higher than that using the wild-type strain. Cyp51A and Cyp51B are 14-α-lanosterol demethylase isozymes in T. rubrum that promote ergosterol biosynthesis and are the targets of azole antifungal drugs. The expression of cyp51A mRNA was induced by the addition of the azole antifungal drug efinaconazole, whereas no such induction was detected for cyp51B, suggesting that Cyp51A functions as an azole-responsive Cyp51 isozyme. To explore the contribution of Cyp51A to susceptibility to azole drugs, the neomycin phosphotransferase (nptII) gene cassette was inserted into the cyp51A 3'-untranslated region of Δku80 to destabilize the mRNA of cyp51A. In this mutant, the induction of cyp51A mRNA expression by efinaconazole was diminished. The minimum inhibitory concentration for several azole drugs of this strain was reduced, suggesting that dermatophyte Cyp51A contributes to the tolerance for azole drugs. These findings suggest that an efficient gene targeting system using Δku80 in T. rubrum is applicable for analyzing genes encoding drug targets.
{"title":"An efficient gene targeting system using Δku80 and functional analysis of Cyp51A in Trichophyton rubrum.","authors":"Masaki Ishii, Tsuyoshi Yamada, Shinya Ohata","doi":"10.1186/s13568-024-01755-8","DOIUrl":"10.1186/s13568-024-01755-8","url":null,"abstract":"<p><p>Trichophyton rubrum is one of the most frequently isolated fungi in patients with dermatophytosis. Despite its clinical significance, the molecular mechanisms of drug resistance and pathogenicity of T. rubrum remain to be elucidated because of the lack of genetic tools, such as efficient gene targeting systems. In this study, we generated a T. rubrum strain that lacks the nonhomologous end-joining-related gene ku80 (Δku80) and then developed a highly efficient genetic recombination system with gene targeting efficiency that was 46 times higher than that using the wild-type strain. Cyp51A and Cyp51B are 14-α-lanosterol demethylase isozymes in T. rubrum that promote ergosterol biosynthesis and are the targets of azole antifungal drugs. The expression of cyp51A mRNA was induced by the addition of the azole antifungal drug efinaconazole, whereas no such induction was detected for cyp51B, suggesting that Cyp51A functions as an azole-responsive Cyp51 isozyme. To explore the contribution of Cyp51A to susceptibility to azole drugs, the neomycin phosphotransferase (nptII) gene cassette was inserted into the cyp51A 3'-untranslated region of Δku80 to destabilize the mRNA of cyp51A. In this mutant, the induction of cyp51A mRNA expression by efinaconazole was diminished. The minimum inhibitory concentration for several azole drugs of this strain was reduced, suggesting that dermatophyte Cyp51A contributes to the tolerance for azole drugs. These findings suggest that an efficient gene targeting system using Δku80 in T. rubrum is applicable for analyzing genes encoding drug targets.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11365917/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103467","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
T and B cell activation are equally important in triggering and orchestrating adaptive host responses to design multi-epitope African swine fever virus (ASFV) vaccines. However, few design methods have considered the trade-off between T and B cell immunogenicity when identifying promising ASFV epitopes. This work proposed a novel Pareto front-based ASFV screening method PFAS to identify promising epitopes for designing multi-epitope vaccines utilizing five ASFV Georgia 2007/1 sequences. To accurately predict T cell immunogenicity, four scoring methods were used to estimate the T cell activation in the four stages, including proteasomal cleavage probability, transporter associated with antigen processing transport efficiency, class I binding affinity of the major histocompatibility complex, and CD8 + cytotoxic T cell immunogenicity. PFAS ranked promising epitopes using a Pareto front method considering T and B cell immunogenicity. The coefficient of determination between the Pareto ranks of multi-epitope vaccines and survival days of swine vaccinations was R2 = 0.95. Consequently, PFAS scored complete epitope profiles and identified 72 promising top-ranked epitopes, including 46 CD2v epitopes, two p30 epitopes, 10 p72 epitopes, and 14 pp220 epitopes. PFAS is the first method of using the Pareto front approach to identify promising epitopes that considers the objectives of maximizing both T and B cell immunogenicity. The top-ranked promising epitopes can be cost-effectively validated in vitro. The Pareto front approach can be adaptively applied to various epitope predictors for bacterial, viral and cancer vaccine developments. The MATLAB code of the Pareto front method was available at https://github.com/NYCU-ICLAB/PFAS .
T 细胞和 B 细胞活化在触发和协调宿主适应性反应以设计多表位非洲猪瘟病毒(ASFV)疫苗方面同等重要。然而,在确定有前景的非洲猪瘟病毒表位时,很少有设计方法考虑到 T 细胞和 B 细胞免疫原性之间的权衡。这项研究提出了一种新颖的基于帕累托前沿的 ASFV 筛选方法 PFAS,利用五个 ASFV Georgia 2007/1 序列来识别有希望的表位,从而设计出多表位疫苗。为了准确预测 T 细胞免疫原性,研究采用了四种评分方法来估算 T 细胞在四个阶段的活化情况,包括蛋白酶体裂解概率、与抗原处理相关的转运体转运效率、主要组织相容性复合体 I 类结合亲和力以及 CD8 + 细胞毒性 T 细胞免疫原性。考虑到 T 细胞和 B 细胞的免疫原性,PFAS 采用帕累托前沿法对有希望的表位进行了排序。多表位疫苗的帕累托排名与猪疫苗接种存活天数之间的决定系数为 R2 = 0.95。因此,PFAS 对完整的表位图谱进行了评分,并确定了 72 个有前途的顶级表位,包括 46 个 CD2v 表位、2 个 p30 表位、10 个 p72 表位和 14 个 pp220 表位。PFAS 是第一种使用帕累托前沿方法来识别有希望的表位的方法,它同时考虑了最大化 T 细胞和 B 细胞免疫原性的目标。排名靠前的有希望的表位可以在体外进行成本效益验证。帕累托前沿方法可以自适应地应用于细菌、病毒和癌症疫苗开发的各种表位预测。帕累托前沿方法的MATLAB代码可在https://github.com/NYCU-ICLAB/PFAS。
{"title":"Multi-epitope vaccine design of African swine fever virus considering T cell and B cell immunogenicity.","authors":"Ting-Yu Chen, Yann-Jen Ho, Fang-Yu Ko, Pei-Yin Wu, Chia-Jung Chang, Shinn-Ying Ho","doi":"10.1186/s13568-024-01749-6","DOIUrl":"10.1186/s13568-024-01749-6","url":null,"abstract":"<p><p>T and B cell activation are equally important in triggering and orchestrating adaptive host responses to design multi-epitope African swine fever virus (ASFV) vaccines. However, few design methods have considered the trade-off between T and B cell immunogenicity when identifying promising ASFV epitopes. This work proposed a novel Pareto front-based ASFV screening method PFAS to identify promising epitopes for designing multi-epitope vaccines utilizing five ASFV Georgia 2007/1 sequences. To accurately predict T cell immunogenicity, four scoring methods were used to estimate the T cell activation in the four stages, including proteasomal cleavage probability, transporter associated with antigen processing transport efficiency, class I binding affinity of the major histocompatibility complex, and CD8 + cytotoxic T cell immunogenicity. PFAS ranked promising epitopes using a Pareto front method considering T and B cell immunogenicity. The coefficient of determination between the Pareto ranks of multi-epitope vaccines and survival days of swine vaccinations was R<sup>2</sup> = 0.95. Consequently, PFAS scored complete epitope profiles and identified 72 promising top-ranked epitopes, including 46 CD2v epitopes, two p30 epitopes, 10 p72 epitopes, and 14 pp220 epitopes. PFAS is the first method of using the Pareto front approach to identify promising epitopes that considers the objectives of maximizing both T and B cell immunogenicity. The top-ranked promising epitopes can be cost-effectively validated in vitro. The Pareto front approach can be adaptively applied to various epitope predictors for bacterial, viral and cancer vaccine developments. The MATLAB code of the Pareto front method was available at https://github.com/NYCU-ICLAB/PFAS .</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11365882/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-31DOI: 10.1186/s13568-024-01751-y
Maryam Pourhajibagher, Zahra Javanmard, Abbas Bahador
Antimicrobial photodynamic therapy (aPDT) is a promising approach to combat antibiotic resistance in endodontic infections. It eliminates residual bacteria from the root canal space and reduces the need for antibiotics. To enhance its effectiveness, an in silico and in vitro study was performed to investigate the potential of targeted aPDT using natural photosensitizers, Kojic acid and Parietin. This approach aims to inhibit the biofilm formation of Enterococcus faecalis, a frequent cause of endodontic infections, by targeting the Ace and Esp proteins. After determining the physicochemical characteristics of Ace and Esp proteins and model quality assessment, the molecular dynamic simulation was performed to recognize the structural variations. The stability and physical movement of the protein-ligand complexes were evaluated. In silico molecular docking was conducted, followed by ADME/Tox profiling, pharmacokinetics characteristics, and assessment of drug-likeness properties of the natural photosensitizers. The study also investigated the changes in the expression of genes (esp and ace) involved in E. faecalis biofilm formation. The results showed that both Kojic acid and Parietin complied with Lipinski's rule of five and exhibited drug-like properties. In silico analysis indicated stable complexes between Ace and Esp proteins and the natural photosensitizers. The molecular docking studies demonstrated good binding affinity. Additionally, the expression of the ace and esp genes was significantly downregulated in aPDT using Kojic acid and Parietin with blue light compared to the control group. This investigation concluded that Kojic acid and Parietin with drug-likeness could efficiently interact with Ace and Esp proteins with a strong binding affinity. Hence, natural photosensitizers-mediated aPDT can be considered a promising adjunctive treatment against endodontic infections.
{"title":"Molecular docking and antimicrobial activities of photoexcited inhibitors in antimicrobial photodynamic therapy against Enterococcus faecalis biofilms in endodontic infections.","authors":"Maryam Pourhajibagher, Zahra Javanmard, Abbas Bahador","doi":"10.1186/s13568-024-01751-y","DOIUrl":"10.1186/s13568-024-01751-y","url":null,"abstract":"<p><p>Antimicrobial photodynamic therapy (aPDT) is a promising approach to combat antibiotic resistance in endodontic infections. It eliminates residual bacteria from the root canal space and reduces the need for antibiotics. To enhance its effectiveness, an in silico and in vitro study was performed to investigate the potential of targeted aPDT using natural photosensitizers, Kojic acid and Parietin. This approach aims to inhibit the biofilm formation of Enterococcus faecalis, a frequent cause of endodontic infections, by targeting the Ace and Esp proteins. After determining the physicochemical characteristics of Ace and Esp proteins and model quality assessment, the molecular dynamic simulation was performed to recognize the structural variations. The stability and physical movement of the protein-ligand complexes were evaluated. In silico molecular docking was conducted, followed by ADME/Tox profiling, pharmacokinetics characteristics, and assessment of drug-likeness properties of the natural photosensitizers. The study also investigated the changes in the expression of genes (esp and ace) involved in E. faecalis biofilm formation. The results showed that both Kojic acid and Parietin complied with Lipinski's rule of five and exhibited drug-like properties. In silico analysis indicated stable complexes between Ace and Esp proteins and the natural photosensitizers. The molecular docking studies demonstrated good binding affinity. Additionally, the expression of the ace and esp genes was significantly downregulated in aPDT using Kojic acid and Parietin with blue light compared to the control group. This investigation concluded that Kojic acid and Parietin with drug-likeness could efficiently interact with Ace and Esp proteins with a strong binding affinity. Hence, natural photosensitizers-mediated aPDT can be considered a promising adjunctive treatment against endodontic infections.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11365891/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142103468","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-28DOI: 10.1186/s13568-024-01754-9
Marta N Mota, Margarida Palma, Isabel Sá-Correia
Methanol is a promising feedstock for biomanufacturing, but the efficiency of methanol-based bioprocesses is limited by the low rate of methanol utilization pathways and methanol toxicity. Yeast diversity is an attractive biological resource to develop efficient bioprocesses since any effort with strain improvement is more deserving if applied to innate robust strains with relevant catabolic and biosynthetic potential. The present study is in line with such rational and describes the isolation and molecular identification of seven isolates of the methylotrophic species Candida boidinii from waters derived from the traditional curation of olives, in different years, and from contaminated superficial soil near fuel stations. The yeast microbiota from those habitats was also characterized. The four C. boidinii isolates obtained from the curation of olives' water exhibited significantly higher maximum specific growth rates (range 0.15-0.19 h-1), compared with the three isolates obtained from the fuel contaminated soils (range 0.05-0.06 h-1) when grown on methanol as the sole C-source (1% (v/v), in shake flasks, at 30°C). The isolates exhibit significant robustness towards methanol toxicity that increases as the cultivation temperature decreases from 30°C to 25°C. The better methanol-based growth performance exhibited by C. boidinii isolates from olives´ soaking waters could not be essentially attributed to higher methanol tolerance. These methanol-efficient catabolizing isolates are proposed as a promising platform to develop methanol-based bioprocesses.
甲醇是一种很有前景的生物制造原料,但由于甲醇利用率低和甲醇毒性,以甲醇为基础的生物工艺的效率受到限制。酵母多样性是开发高效生物工艺的一种极具吸引力的生物资源,因为任何菌株改良工作如果应用于具有相关分解代谢和生物合成潜力的先天强健菌株,都会更有价值。本研究正是基于这一原理,描述了从不同年份的传统橄榄加工水域和加油站附近受污染的表层土壤中分离和分子鉴定出的 7 个滋养甲基念珠菌菌种 Candida boidinii。对这些生境中的酵母微生物群也进行了特征描述。在以甲醇为唯一 C 源(1%(v/v),摇瓶,30°C)的条件下生长时,与从燃料污染土壤中获得的三个分离物(0.05-0.06 h-1)相比,从橄榄腌制水中获得的四个 C. boidinii 分离物的最大特定生长率(0.15-0.19 h-1)明显更高。随着培养温度从 30°C 降至 25°C,分离物对甲醇毒性的耐受性明显增强。从橄榄浸泡水中分离出的 C. boidinii 在甲醇基础上表现出更好的生长性能,但这并不能完全归因于较高的甲醇耐受性。建议将这些甲醇高效分解分离物作为开发基于甲醇的生物工艺的理想平台。
{"title":"Candida boidinii isolates from olive curation water: a promising platform for methanol-based biomanufacturing.","authors":"Marta N Mota, Margarida Palma, Isabel Sá-Correia","doi":"10.1186/s13568-024-01754-9","DOIUrl":"10.1186/s13568-024-01754-9","url":null,"abstract":"<p><p>Methanol is a promising feedstock for biomanufacturing, but the efficiency of methanol-based bioprocesses is limited by the low rate of methanol utilization pathways and methanol toxicity. Yeast diversity is an attractive biological resource to develop efficient bioprocesses since any effort with strain improvement is more deserving if applied to innate robust strains with relevant catabolic and biosynthetic potential. The present study is in line with such rational and describes the isolation and molecular identification of seven isolates of the methylotrophic species Candida boidinii from waters derived from the traditional curation of olives, in different years, and from contaminated superficial soil near fuel stations. The yeast microbiota from those habitats was also characterized. The four C. boidinii isolates obtained from the curation of olives' water exhibited significantly higher maximum specific growth rates (range 0.15-0.19 h<sup>-1</sup>), compared with the three isolates obtained from the fuel contaminated soils (range 0.05-0.06 h<sup>-1</sup>) when grown on methanol as the sole C-source (1% (v/v), in shake flasks, at 30°C). The isolates exhibit significant robustness towards methanol toxicity that increases as the cultivation temperature decreases from 30°C to 25°C. The better methanol-based growth performance exhibited by C. boidinii isolates from olives´ soaking waters could not be essentially attributed to higher methanol tolerance. These methanol-efficient catabolizing isolates are proposed as a promising platform to develop methanol-based bioprocesses.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11358584/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142091416","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-08-16DOI: 10.1186/s13568-024-01746-9
Omima Elkhateeb, Mohamed B Atta, Esawy Mahmoud
The biosynthesis of iron oxide nanoparticles has received increasing attention in the field of food nanotechnology because of their non-toxicity, high efficiency, high antibacterial power, and decontamination features. Therefore, biosynthesis of iron oxide nanoparticles (nFe) was prepared from the leaves of some vegetables, such as cabbage (C) and turnips (T), as well as moringa leaves (M). Alcoholic extracts of these nanoparticles were also tested on Staphylococcus aureus and Escherichia coli to evaluate their antibacterial activity. The results revealed that the particle sizes of the biosynthesis nanomaterials studied ranged from 12.99 to 22.72 nm, and the particles were spherical, irregular, and surrounded by black color. It also contains many functional groups and minerals. Iron nanoparticles modified with Moringa oleifera extract at a concentration of 200 ppm had the highest phenol content compared to other biosynthesis nanoparticles studied. TnFe and MnFe at 200 ppm had a maximum zone of inhibition of 25 mm and 24 mm against Staphylococcus aureus and Escherichia coli, respectively. While the minimum inhibition zone of 8.0 mm was observed at 25 ppm for nFe against Escherichia coli. Therefore, it is recommended to use these extracts of biosynthesis iron oxide nanoparticles as antibacterial agents for stored foods.
{"title":"Biosynthesis of iron oxide nanoparticles using plant extracts and evaluation of their antibacterial activity.","authors":"Omima Elkhateeb, Mohamed B Atta, Esawy Mahmoud","doi":"10.1186/s13568-024-01746-9","DOIUrl":"10.1186/s13568-024-01746-9","url":null,"abstract":"<p><p>The biosynthesis of iron oxide nanoparticles has received increasing attention in the field of food nanotechnology because of their non-toxicity, high efficiency, high antibacterial power, and decontamination features. Therefore, biosynthesis of iron oxide nanoparticles (nFe) was prepared from the leaves of some vegetables, such as cabbage (C) and turnips (T), as well as moringa leaves (M). Alcoholic extracts of these nanoparticles were also tested on Staphylococcus aureus and Escherichia coli to evaluate their antibacterial activity. The results revealed that the particle sizes of the biosynthesis nanomaterials studied ranged from 12.99 to 22.72 nm, and the particles were spherical, irregular, and surrounded by black color. It also contains many functional groups and minerals. Iron nanoparticles modified with Moringa oleifera extract at a concentration of 200 ppm had the highest phenol content compared to other biosynthesis nanoparticles studied. TnFe and MnFe at 200 ppm had a maximum zone of inhibition of 25 mm and 24 mm against Staphylococcus aureus and Escherichia coli, respectively. While the minimum inhibition zone of 8.0 mm was observed at 25 ppm for nFe against Escherichia coli. Therefore, it is recommended to use these extracts of biosynthesis iron oxide nanoparticles as antibacterial agents for stored foods.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.5,"publicationDate":"2024-08-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11329484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141995098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}