Pub Date : 2024-03-18DOI: 10.1186/s13568-024-01682-8
Juan Long, Yang Zeng, Fei Liang, Nan Liu, Yongzhi Xi, Yuying Sun, Xiao Zhao
{"title":"Correction to: Transformed Salmonella typhimurium SL7207/pcDNA-CCOL2A1 as an orally administered DNA vaccine.","authors":"Juan Long, Yang Zeng, Fei Liang, Nan Liu, Yongzhi Xi, Yuying Sun, Xiao Zhao","doi":"10.1186/s13568-024-01682-8","DOIUrl":"10.1186/s13568-024-01682-8","url":null,"abstract":"","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10948640/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140157307","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 : 2024-03-15DOI: 10.1186/s13568-024-01685-5
Jeong Eun Kwon, Woojae Hong, Hyelin Jeon, Cha Soon Kim, Hyunggun Kim, Se Chan Kang
This study aimed to identify substances including Lactobacillus rhamnosus vitaP1 (KACC 92054P) that alleviate hangover-induced emotional anxiety and liver damage. The association between emotional anxiety caused by hangover and the genes P2X4, P2X7, SLC6A4 was investigated. In vitro and in vivo analyses were conducted to assess the influence of free-panica on alcohol-induced upregulated gene expression. Additionally, the concentration of AST, ALT, alcohol, and acetaldehyde in blood was measured. Free-panica, consisting of five natural products (Phyllanthus amarus, Phoenix dactylifera, Vitis vinifera, Zingiber officinale, and Lactobacillus rhamnosus), were evaluated for their regulatory effects on genes involved in alcohol-induced emotional anxiety and liver damage. The combination of these natural products in free-panica successfully restored emotional anxiety, and the concentration of AST, ALT, alcohol, and acetaldehyde in blood to those of the normal control group. These findings support the potential development of free-panica as a health functional food or medicinal intervention for relieving hangover symptoms and protecting liver from alcohol consumption.
{"title":"Suppression of P2X4 and P2X7 by Lactobacillus rhamnosus vitaP1: effects on hangover symptoms.","authors":"Jeong Eun Kwon, Woojae Hong, Hyelin Jeon, Cha Soon Kim, Hyunggun Kim, Se Chan Kang","doi":"10.1186/s13568-024-01685-5","DOIUrl":"10.1186/s13568-024-01685-5","url":null,"abstract":"<p><p>This study aimed to identify substances including Lactobacillus rhamnosus vitaP1 (KACC 92054P) that alleviate hangover-induced emotional anxiety and liver damage. The association between emotional anxiety caused by hangover and the genes P2X4, P2X7, SLC6A4 was investigated. In vitro and in vivo analyses were conducted to assess the influence of free-panica on alcohol-induced upregulated gene expression. Additionally, the concentration of AST, ALT, alcohol, and acetaldehyde in blood was measured. Free-panica, consisting of five natural products (Phyllanthus amarus, Phoenix dactylifera, Vitis vinifera, Zingiber officinale, and Lactobacillus rhamnosus), were evaluated for their regulatory effects on genes involved in alcohol-induced emotional anxiety and liver damage. The combination of these natural products in free-panica successfully restored emotional anxiety, and the concentration of AST, ALT, alcohol, and acetaldehyde in blood to those of the normal control group. These findings support the potential development of free-panica as a health functional food or medicinal intervention for relieving hangover symptoms and protecting liver from alcohol consumption.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10942966/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140139709","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 : 2024-03-11DOI: 10.1186/s13568-024-01684-6
Maryam Pourhajibagher, Abbas Bahador
The presence of oropharyngeal human papillomavirus (HPV)-18 E6 and E7 oncoproteins is highly significant in the progression of oropharyngeal cancer. Natural flavonoid compounds have potential as photosensitizers for light-activated antimicrobial therapy against HPV-associated oropharyngeal cancer. This study evaluated five natural flavonoid glycosides including Fisetin, Kaempferol, Morin, Myricetin, and Quercetin as photosensitizers against HPV-18 E6 and E7 oncoproteins using computational methods. After obtaining the amino acid sequences of HPV-18 E6 and E7, various tools were used to predict and verify their properties. The PubChem database was then examined to identify potential natural flavonoid glycosides, followed by predictions of their drug-likeness and ADMET properties. Subsequently, molecular docking was conducted to enhance the screening accuracy and to gain insights into the interactions between the natural compounds and the active sites of HPV-18 E6 and E7 oncoproteins. The protein structures of E6 and E7 were predicted and validated to be reliable. The results of molecular docking demonstrated that Kaempferol exhibited the highest binding affinity to both E6 and E7. All compounds satisfied Lipinski's rules of drug-likeness, except Myricetin. They showed high absorption, distribution volume and similar ADMET profiles with no toxicity. In summary, natural flavonoid glycosides, especially Kaempferol, show potential as photosensitizers for antimicrobial photodynamic therapy against HPV-associated oropharyngeal cancer through inhibition of E6 and E7 oncoproteins. These findings provide insights into the development of novel therapeutic strategies based on antimicrobial photodynamic therapy.
{"title":"Bioinformatics analysis of photoexcited natural flavonoid glycosides as the inhibitors for oropharyngeal HPV oncoproteins","authors":"Maryam Pourhajibagher, Abbas Bahador","doi":"10.1186/s13568-024-01684-6","DOIUrl":"https://doi.org/10.1186/s13568-024-01684-6","url":null,"abstract":"<p>The presence of oropharyngeal human papillomavirus (HPV)-18 E6 and E7 oncoproteins is highly significant in the progression of oropharyngeal cancer. Natural flavonoid compounds have potential as photosensitizers for light-activated antimicrobial therapy against HPV-associated oropharyngeal cancer. This study evaluated five natural flavonoid glycosides including Fisetin, Kaempferol, Morin, Myricetin, and Quercetin as photosensitizers against HPV-18 E6 and E7 oncoproteins using computational methods. After obtaining the amino acid sequences of HPV-18 E6 and E7, various tools were used to predict and verify their properties. The PubChem database was then examined to identify potential natural flavonoid glycosides, followed by predictions of their drug-likeness and ADMET properties. Subsequently, molecular docking was conducted to enhance the screening accuracy and to gain insights into the interactions between the natural compounds and the active sites of HPV-18 E6 and E7 oncoproteins. The protein structures of E6 and E7 were predicted and validated to be reliable. The results of molecular docking demonstrated that Kaempferol exhibited the highest binding affinity to both E6 and E7. All compounds satisfied Lipinski's rules of drug-likeness, except Myricetin. They showed high absorption, distribution volume and similar ADMET profiles with no toxicity. In summary, natural flavonoid glycosides, especially Kaempferol, show potential as photosensitizers for antimicrobial photodynamic therapy against HPV-associated oropharyngeal cancer through inhibition of E6 and E7 oncoproteins. These findings provide insights into the development of novel therapeutic strategies based on antimicrobial photodynamic therapy.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140098543","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 : 2024-02-24DOI: 10.1186/s13568-024-01668-6
Wang Ying, Cai Chunjing, Lu Junhua, Li Xuan, Wang Zhaojiang, Chu Jie
Lignin is main composition of agricultural biomass which can be decomposed through enzymatic hydrolysis by fungi. However, there are still needs to identify more efficient and effective fungal stain for biomass valorization. In this study, lignin degrading fungi from birch forest were screened for sustainable degradation of waste agricultural straws. The most effective strain was identified as Cerrena unicolor GC.u01 using 18 S rDNA gene-sequencing technology. Three different crop straws (corn stalk, rice and wheat straws) were used for the biotreatment studies. The activities of lignin degrading enzymes, laccase (Lac), cellulase and xylanase, secreted by C. unicolor were also determined. Scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FTIR) and thermal gravimetric analyzer (TGA) were further used to monitor the effects of the biotreatment process. The results showed that C. unicolor degraded 34.3% rice straw lignin, a percentage which was higher than other isolated strains after 15 d straw liquid fermentation. The highest Lac activity (8.396 U•mL- 1) was observed with corn stalk on the 7 d. Cellulase and xylanase activities, in the same biomass, were higher than those of wheat and rice straws after 15 d. Furthermore, SEM, FTIR and TGA analyses showed that C. unicolor pretreatment process had significant effects on corn stalk, rice and wheat straws' structures. The newly isolated stain of C. unicolor demonstrated high lignin degradation potential that can provide effective, ecofriendly means of valorizing biomass to industrial useable raw-material.
木质素是农业生物质的主要成分,可以通过真菌的酶水解作用进行分解。然而,在生物质的价值化方面,仍然需要找到更高效、更有效的真菌染色剂。本研究筛选了桦树林中的木质素降解真菌,用于废弃农作物秸秆的可持续降解。利用 18 S rDNA 基因测序技术,确定了最有效的菌株为 Cerrena unicolor GC.u01。生物处理研究使用了三种不同的农作物秸秆(玉米秸秆、水稻秸秆和小麦秸秆)。此外,还测定了 C. unicolor 分泌的木质素降解酶、漆酶(Lac)、纤维素酶和木聚糖酶的活性。扫描电子显微镜(SEM)、傅立叶变换红外光谱(FTIR)和热重分析仪(TGA)被进一步用于监测生物处理过程的效果。结果表明,经过 15 天的秸秆液体发酵后,C. unicolor 降解了 34.3% 的稻草木质素,这一比例高于其他分离菌株。此外,扫描电镜、傅立叶变换红外光谱和热重分析表明,单色杆菌预处理过程对玉米秸秆、水稻和小麦秸秆的结构有显著影响。新分离出的 C. unicolor 染色体具有很高的木质素降解潜力,可为生物质转化为工业可用原料提供有效、生态友好的方法。
{"title":"Efficient crop straws biotreatment using the fungus Cerrena Unicolor GC.u01.","authors":"Wang Ying, Cai Chunjing, Lu Junhua, Li Xuan, Wang Zhaojiang, Chu Jie","doi":"10.1186/s13568-024-01668-6","DOIUrl":"10.1186/s13568-024-01668-6","url":null,"abstract":"<p><p>Lignin is main composition of agricultural biomass which can be decomposed through enzymatic hydrolysis by fungi. However, there are still needs to identify more efficient and effective fungal stain for biomass valorization. In this study, lignin degrading fungi from birch forest were screened for sustainable degradation of waste agricultural straws. The most effective strain was identified as Cerrena unicolor GC.u01 using 18 S rDNA gene-sequencing technology. Three different crop straws (corn stalk, rice and wheat straws) were used for the biotreatment studies. The activities of lignin degrading enzymes, laccase (Lac), cellulase and xylanase, secreted by C. unicolor were also determined. Scanning electron microscopy (SEM), fourier transform infrared spectroscopy (FTIR) and thermal gravimetric analyzer (TGA) were further used to monitor the effects of the biotreatment process. The results showed that C. unicolor degraded 34.3% rice straw lignin, a percentage which was higher than other isolated strains after 15 d straw liquid fermentation. The highest Lac activity (8.396 U•mL<sup>- 1</sup>) was observed with corn stalk on the 7 d. Cellulase and xylanase activities, in the same biomass, were higher than those of wheat and rice straws after 15 d. Furthermore, SEM, FTIR and TGA analyses showed that C. unicolor pretreatment process had significant effects on corn stalk, rice and wheat straws' structures. The newly isolated stain of C. unicolor demonstrated high lignin degradation potential that can provide effective, ecofriendly means of valorizing biomass to industrial useable raw-material.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10894188/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139943676","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 : 2024-02-21DOI: 10.1186/s13568-024-01678-4
Aala A Abulfaraj, Ashwag Y Shami, Nahaa M Alotaibi, Maryam M Alomran, Abeer S Aloufi, Abeer Al-Andal, Nawwaf R AlHamdan, Fatimah M Alshehrei, Fatmah O Sefrji, Khloud H Alsaadi, Haneen W Abuauf, Sahar A Alshareef, Rewaa S Jalal
The operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The ultimate goal underlying root exudation, as surmised from the present investigation, was the biosynthesis of saccharides, amino acids, and nucleic acids, which are imperative for the sustenance, propagation, or reproduction of microbial consortia. The symbiotic companionship existing between the wild plant and its associated rhizobiome amplifies the resilience of the microbial community against adverse abiotic stresses, achieved through the orchestration of ABA (abscisic acid) signaling and its cascading downstream effects. Emergent from the process of exudation are pivotal bioactive compounds including ATP, D-ribose, pyruvate, glucose, glutamine, and thiamine diphosphate. In conclusion, we hypothesize that future efforts to enhance the growth and productivity of commercially important crop plants under both favorable and unfavorable environmental conditions may focus on manipulating plant rhizobiomes.
{"title":"Exploration of genes encoding KEGG pathway enzymes in rhizospheric microbiome of the wild plant Abutilon fruticosum.","authors":"Aala A Abulfaraj, Ashwag Y Shami, Nahaa M Alotaibi, Maryam M Alomran, Abeer S Aloufi, Abeer Al-Andal, Nawwaf R AlHamdan, Fatimah M Alshehrei, Fatmah O Sefrji, Khloud H Alsaadi, Haneen W Abuauf, Sahar A Alshareef, Rewaa S Jalal","doi":"10.1186/s13568-024-01678-4","DOIUrl":"10.1186/s13568-024-01678-4","url":null,"abstract":"<p><p>The operative mechanisms and advantageous synergies existing between the rhizobiome and the wild plant species Abutilon fruticosum were studied. Within the purview of this scientific study, the reservoir of genes in the rhizobiome, encoding the most highly enriched enzymes, was dominantly constituted by members of phylum Thaumarchaeota within the archaeal kingdom, phylum Proteobacteria within the bacterial kingdom, and the phylum Streptophyta within the eukaryotic kingdom. The ensemble of enzymes encoded through plant exudation exhibited affiliations with 15 crosstalking KEGG (Kyoto Encyclopaedia of Genes and Genomes) pathways. The ultimate goal underlying root exudation, as surmised from the present investigation, was the biosynthesis of saccharides, amino acids, and nucleic acids, which are imperative for the sustenance, propagation, or reproduction of microbial consortia. The symbiotic companionship existing between the wild plant and its associated rhizobiome amplifies the resilience of the microbial community against adverse abiotic stresses, achieved through the orchestration of ABA (abscisic acid) signaling and its cascading downstream effects. Emergent from the process of exudation are pivotal bioactive compounds including ATP, D-ribose, pyruvate, glucose, glutamine, and thiamine diphosphate. In conclusion, we hypothesize that future efforts to enhance the growth and productivity of commercially important crop plants under both favorable and unfavorable environmental conditions may focus on manipulating plant rhizobiomes.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10881953/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139911851","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 : 2024-02-20DOI: 10.1186/s13568-024-01674-8
Bharati Naik, Jayaprakash Sasikumar, Vishal B, Shankar Prasad Das
Evidence of fungal coexistence in humans points towards fungal adaptation to the host environment, like the skin. The human commensal Malassezia has evolved, especially residing in sebum-rich areas of the mammalian body where it can get the necessary nutrition for its survival. This fungus is primarily responsible for skin diseases like Pityriasis versicolor (PV), characterized by hypo or hyperpigmented skin discoloration and erythematous macules. In this manuscript, we report a 19-year-old healthy female who presented with a one-year history of reddish, hypopigmented, asymptomatic lesions over the chest and a raised erythematous lesion over the face. Upon clinical observation, the patient displayed multiple erythematous macules and erythematous papules over the bilateral malar area of the face, along with multiple hypopigmented scaly macules present on the chest and back. Based on the above clinical findings, a diagnosis of PV and Acne vulgaris (AV) was made. Interestingly, the patient was immunocompetent and didn't have any comorbidities. Upon isolation of skin scrapings and post-culturing, we found the existence of three fungal genera in the same region of the patient's body. We further went on to confirm the identity of the particular species and found it to represent Malassezia, Rhodotorula, and Candida. We report how Malassezia, the predominant microbial resident skin fungus, coexists with other fungal members of the skin mycobiome. This study on an applied aspect of microbiology also shows how important it is to identify the fungal organism associated with skin infections so that appropriate therapeutics can be advised to avoid cases of relapse.
{"title":"Fungal coexistence in the skin mycobiome: a study involving Malassezia, Candida, and Rhodotorula.","authors":"Bharati Naik, Jayaprakash Sasikumar, Vishal B, Shankar Prasad Das","doi":"10.1186/s13568-024-01674-8","DOIUrl":"10.1186/s13568-024-01674-8","url":null,"abstract":"<p><p>Evidence of fungal coexistence in humans points towards fungal adaptation to the host environment, like the skin. The human commensal Malassezia has evolved, especially residing in sebum-rich areas of the mammalian body where it can get the necessary nutrition for its survival. This fungus is primarily responsible for skin diseases like Pityriasis versicolor (PV), characterized by hypo or hyperpigmented skin discoloration and erythematous macules. In this manuscript, we report a 19-year-old healthy female who presented with a one-year history of reddish, hypopigmented, asymptomatic lesions over the chest and a raised erythematous lesion over the face. Upon clinical observation, the patient displayed multiple erythematous macules and erythematous papules over the bilateral malar area of the face, along with multiple hypopigmented scaly macules present on the chest and back. Based on the above clinical findings, a diagnosis of PV and Acne vulgaris (AV) was made. Interestingly, the patient was immunocompetent and didn't have any comorbidities. Upon isolation of skin scrapings and post-culturing, we found the existence of three fungal genera in the same region of the patient's body. We further went on to confirm the identity of the particular species and found it to represent Malassezia, Rhodotorula, and Candida. We report how Malassezia, the predominant microbial resident skin fungus, coexists with other fungal members of the skin mycobiome. This study on an applied aspect of microbiology also shows how important it is to identify the fungal organism associated with skin infections so that appropriate therapeutics can be advised to avoid cases of relapse.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10879058/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139904821","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 : 2024-02-15DOI: 10.1186/s13568-024-01679-3
Mengting Li, Shuhong Gao, Pengcheng Yang, Hejin Li
To enhance the ribonucleic acid (RNA) productivity for industrial applications, this study employed strain screening and medium optimization to improve the content of RNA in Cyberlindnera jadinii. A rapid screening method, combining atmospheric and room temperature plasma mutagenesis, 48-deep-well plates fermentation, and microplate reader detection, was developed. A mutant strain named WB15 with high RNA content was successfully obtained, exhibiting the RNA content of 156 ± 4.5 mg/g DCW, 1.4 times of the starting strain CCTCC AY 92020. Furthermore, Plackett-Burman design and response surface methodology were employed to identify three significant factors (yeast extract, soybean peptone, and KH2PO4) affecting the RNA content. By utilizing the optimal medium composed of 13.43 g/L yeast extract, 12.12 g/L soybean peptone and 2.78 g/L KH2PO4, the RNA content of WB15 further increased to 184 ± 4.9 mg/g DCW. Additionally, the mutant strain WB15 exhibited a greater cellular width compared to AY 92020, along with increased growth rate and single-cell RNA content by 22% and 48.9%, respectively. Perturbations in ribosome assembly, specifically a reduction in the ratio of ribosomal proteins to ribosomal RNA of the large subunit, might indirectly contribute to the higher RNA content in the WB15 strain. Overall, the combination of rapid screening with fermentation medium optimization proved to be an effective approach for improving the RNA content of C. jadinii, thus facilitating the industrial production of RNA.
{"title":"Improvement of ribonucleic acid production in Cyberlindnera jadinii and optimization of fermentation medium.","authors":"Mengting Li, Shuhong Gao, Pengcheng Yang, Hejin Li","doi":"10.1186/s13568-024-01679-3","DOIUrl":"10.1186/s13568-024-01679-3","url":null,"abstract":"<p><p>To enhance the ribonucleic acid (RNA) productivity for industrial applications, this study employed strain screening and medium optimization to improve the content of RNA in Cyberlindnera jadinii. A rapid screening method, combining atmospheric and room temperature plasma mutagenesis, 48-deep-well plates fermentation, and microplate reader detection, was developed. A mutant strain named WB15 with high RNA content was successfully obtained, exhibiting the RNA content of 156 ± 4.5 mg/g DCW, 1.4 times of the starting strain CCTCC AY 92020. Furthermore, Plackett-Burman design and response surface methodology were employed to identify three significant factors (yeast extract, soybean peptone, and KH<sub>2</sub>PO<sub>4</sub>) affecting the RNA content. By utilizing the optimal medium composed of 13.43 g/L yeast extract, 12.12 g/L soybean peptone and 2.78 g/L KH<sub>2</sub>PO<sub>4</sub>, the RNA content of WB15 further increased to 184 ± 4.9 mg/g DCW. Additionally, the mutant strain WB15 exhibited a greater cellular width compared to AY 92020, along with increased growth rate and single-cell RNA content by 22% and 48.9%, respectively. Perturbations in ribosome assembly, specifically a reduction in the ratio of ribosomal proteins to ribosomal RNA of the large subunit, might indirectly contribute to the higher RNA content in the WB15 strain. Overall, the combination of rapid screening with fermentation medium optimization proved to be an effective approach for improving the RNA content of C. jadinii, thus facilitating the industrial production of RNA.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10869677/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139734240","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 : 2024-02-15DOI: 10.1186/s13568-024-01673-9
Santasree Sarma Biswas, Jayanti Datta Roy
The number of infections and deaths caused by multidrug resistant (MDR) tuberculosis is increasing globally. One of the efflux pumps, that makes Mycobacterium tuberculosis resistant to a number of antibiotics and results in unfavourable treatment results is Tap or Rv1258c. In our study, we tried to utilize a rational drug design technique using in silico approach to look for an efficient and secure efflux pump inhibitor (EPI) against Rv1258c. The structure of Rv1258c was built using the homology modeling tool MODELLER 9.24. 210 phytocompounds were used for blind and site-specific ligand docking against the modelled structure of Rv1258c using AutoDock Vina software. The best docked plant compounds were further analysed for druglikeness and toxicity. In addition to having excellent docking scores, two plant compounds-ellagic acid and baicalein-also exhibited highly desirable drug-like qualities. These substances outperform more well-known EPIs like piperine and verapamil in terms of effectiveness. This data shows that these two compounds might be further investigated for their potential as Rv1258c inhibitors.
{"title":"Phytocompounds as potential inhibitors of mycobacterial multidrug efflux pump Rv1258c: an in silico approach.","authors":"Santasree Sarma Biswas, Jayanti Datta Roy","doi":"10.1186/s13568-024-01673-9","DOIUrl":"10.1186/s13568-024-01673-9","url":null,"abstract":"<p><p>The number of infections and deaths caused by multidrug resistant (MDR) tuberculosis is increasing globally. One of the efflux pumps, that makes Mycobacterium tuberculosis resistant to a number of antibiotics and results in unfavourable treatment results is Tap or Rv1258c. In our study, we tried to utilize a rational drug design technique using in silico approach to look for an efficient and secure efflux pump inhibitor (EPI) against Rv1258c. The structure of Rv1258c was built using the homology modeling tool MODELLER 9.24. 210 phytocompounds were used for blind and site-specific ligand docking against the modelled structure of Rv1258c using AutoDock Vina software. The best docked plant compounds were further analysed for druglikeness and toxicity. In addition to having excellent docking scores, two plant compounds-ellagic acid and baicalein-also exhibited highly desirable drug-like qualities. These substances outperform more well-known EPIs like piperine and verapamil in terms of effectiveness. This data shows that these two compounds might be further investigated for their potential as Rv1258c inhibitors.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10869325/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139740171","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 : 2024-02-14DOI: 10.1186/s13568-024-01677-5
Fatemeh Afraei, Sara Daneshjou, Bahareh Dabirmanesh
The bacterial enzyme chondroitinase ABCI (chABCI), which has been isolated from Proteus Vulgaris, is crucial in the treatment of spinal cord injuries. However, due to its short lifespan, the maintenance and clinical application of this enzyme are very constrained. In this study, the immobilization of this enzyme on hydroxyapatite has been carried out and assessed with the aim of enhancing the characteristics and efficiency of chABCI. Hydroxyapatite particles (HAPs) are a potential candidate for drug-delivery carriers because of their excellent biocompatibility, shape controllability, and high adsorption. The use of the nanometer scale allows efficient access to the enzyme's substrate. It demonstrates important biological application capabilities in this way. Field emission gun-scanning electron microscopy (FEG-SEM), X-ray diffraction (XRD), infrared spectroscopy (FT-IR), in vitro release study, and cytotoxicity test were used to characterize the drug nanosystem's properties. According to the findings, electrostatic bindings was formed between charged groups of the enzyme and hydroxyapatite nanoparticles. The results also demonstrated that immobilized chABCI on hydroxyapatite has beneficial properties, such as more manageable drug release, minimal toxicity and side effects, and a high potential to enhance the efficacy of drug delivery and decrease the need for repeated injections.
{"title":"Synthesis and evaluation of nanosystem containing chondroitinase ABCI based on hydroxyapatite.","authors":"Fatemeh Afraei, Sara Daneshjou, Bahareh Dabirmanesh","doi":"10.1186/s13568-024-01677-5","DOIUrl":"10.1186/s13568-024-01677-5","url":null,"abstract":"<p><p>The bacterial enzyme chondroitinase ABCI (chABCI), which has been isolated from Proteus Vulgaris, is crucial in the treatment of spinal cord injuries. However, due to its short lifespan, the maintenance and clinical application of this enzyme are very constrained. In this study, the immobilization of this enzyme on hydroxyapatite has been carried out and assessed with the aim of enhancing the characteristics and efficiency of chABCI. Hydroxyapatite particles (HAPs) are a potential candidate for drug-delivery carriers because of their excellent biocompatibility, shape controllability, and high adsorption. The use of the nanometer scale allows efficient access to the enzyme's substrate. It demonstrates important biological application capabilities in this way. Field emission gun-scanning electron microscopy (FEG-SEM), X-ray diffraction (XRD), infrared spectroscopy (FT-IR), in vitro release study, and cytotoxicity test were used to characterize the drug nanosystem's properties. According to the findings, electrostatic bindings was formed between charged groups of the enzyme and hydroxyapatite nanoparticles. The results also demonstrated that immobilized chABCI on hydroxyapatite has beneficial properties, such as more manageable drug release, minimal toxicity and side effects, and a high potential to enhance the efficacy of drug delivery and decrease the need for repeated injections.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10866842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139728743","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}
This study aimed to evaluate the interaction between methicillin-resistant Staphylococcus aureus(MRSA) and Candida spp. in the oral cavity of children with malignancies under chemotherapy. We evaluated the expression level of Als3p and mecA in Candida spp. and MRSA strains in both single colonization and co-colonization condition. Oral and nasal samples were collected by dry sponge swabs in 10 ml of sterile phosphate-buffered saline. The MRSA and Candida spp. was confirmed using the PCR method and mecA and Als3p genes, respectively. The SYBR Green-based quantitative real-time PCR was used to evaluate the relative expression levels of mecA and Als3p genes in MRSA and Candida spp., respectively. The frequency of S. aureus in oral-only and nasal-only swab samples were 14.1% (n = 24/170). 58.3% (n = 14/24) and 29.2% (n = 7/24) of S. aureus isolated from oral and nasal samples were MRSA, respectively. Among Candida species, C. albicans (n = 28/170; 16.5%) had the highest frequency. The oral co-colonization of MRSA and Candida spp. was detected in 4.7% (n = 8/170) patients. The overall average of gene expression levels among all Candida spp. and MRSA isolates indicated that the mecA and Als3p genes expression increased six and two times in co-colonization conditions compared to single colonization conditions, respectively. Our findings revealed the importance of polymicrobial infection in clinical settings and stated that it is possible that Candida spp. facilitates the infection of S. aureus and can lead to systemic infection in co-colonized patients.
{"title":"Co-colonization of methicillin-resistant Staphylococcus aureus and Candida spp. in children with malignancies.","authors":"Raziyeh Baharvand, Fatemeh Fallah, Parvaneh Jafari, Leila Azimi","doi":"10.1186/s13568-024-01667-7","DOIUrl":"10.1186/s13568-024-01667-7","url":null,"abstract":"<p><p>This study aimed to evaluate the interaction between methicillin-resistant Staphylococcus aureus(MRSA) and Candida spp. in the oral cavity of children with malignancies under chemotherapy. We evaluated the expression level of Als3p and mecA in Candida spp. and MRSA strains in both single colonization and co-colonization condition. Oral and nasal samples were collected by dry sponge swabs in 10 ml of sterile phosphate-buffered saline. The MRSA and Candida spp. was confirmed using the PCR method and mecA and Als3p genes, respectively. The SYBR Green-based quantitative real-time PCR was used to evaluate the relative expression levels of mecA and Als3p genes in MRSA and Candida spp., respectively. The frequency of S. aureus in oral-only and nasal-only swab samples were 14.1% (n = 24/170). 58.3% (n = 14/24) and 29.2% (n = 7/24) of S. aureus isolated from oral and nasal samples were MRSA, respectively. Among Candida species, C. albicans (n = 28/170; 16.5%) had the highest frequency. The oral co-colonization of MRSA and Candida spp. was detected in 4.7% (n = 8/170) patients. The overall average of gene expression levels among all Candida spp. and MRSA isolates indicated that the mecA and Als3p genes expression increased six and two times in co-colonization conditions compared to single colonization conditions, respectively. Our findings revealed the importance of polymicrobial infection in clinical settings and stated that it is possible that Candida spp. facilitates the infection of S. aureus and can lead to systemic infection in co-colonized patients.</p>","PeriodicalId":7537,"journal":{"name":"AMB Express","volume":null,"pages":null},"PeriodicalIF":3.7,"publicationDate":"2024-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10864235/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139728741","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}