Pub Date : 2023-08-26DOI: 10.15625/1811-4989/17659
D. T. Tuyen, Vu Thanh Tung, Nguyễn Nhật Linh, Le Thanh Hoang, Nguyen Le Thanh, Nguyen Thi Anh Tuyet, Nguyen Thi Thao, Nguyen Thi Hien Trang, Nguyen Thi Trung, Luu Minh Duc, Dao Thi Mai Anh
Xylanase A of Aspergillus niger dsm 1957 was successfully expressed in strain Pichia pastoris GS115/pXlnA in YP medium induced by methanol. Molecular weight of the recombinant xylanase A was 35 kDa, that was consistent with the theoretical calculation and the enzyme activity in the culture was 7310 U/mL. Maximal xylanase activity (11180 U/mL) was gained after culturing the recombinant yeast for 120 hours in the present of 1% methanol. Among of seven media (BMMY, MMY, MM, YPM, YPTM, YPTCM, and YP) utilized for the yeast culture, the highest activity of the produced recombinant xylanase A (21620 U/mL) was reached in BMMY medium, while the lowest activity (1410 U/mL) was found in YPTCM medium. At the appropriate conditions, the recombinant xylanase A activity was 2.96 folds higher than that expressed in normal conditions. The conditions for recombinant xylanase A enzymatic hydrolysis of several agricultural wastes were also investigated. The results showed that in appropriate conditions (40oC, 24 hours, substrate concentration of 40 mg), the highest amount of reducing sugars produced from cob, rice bran and soybean meal substrates were 0.617 ± 0.002 μmol/mL, 0.663 ± 0.002 μmol/mL, and 0.814 ± 0.003 μmol/mL, respectively. Overall, with these distinctive properties, the recombinant xylanase A may initially become a potential candidate for various industrial applications.
{"title":"Investigation of culture conditions for recombinant xylanase a production and its enzymatic hydrolysis of agricultural wastes","authors":"D. T. Tuyen, Vu Thanh Tung, Nguyễn Nhật Linh, Le Thanh Hoang, Nguyen Le Thanh, Nguyen Thi Anh Tuyet, Nguyen Thi Thao, Nguyen Thi Hien Trang, Nguyen Thi Trung, Luu Minh Duc, Dao Thi Mai Anh","doi":"10.15625/1811-4989/17659","DOIUrl":"https://doi.org/10.15625/1811-4989/17659","url":null,"abstract":"Xylanase A of Aspergillus niger dsm 1957 was successfully expressed in strain Pichia pastoris GS115/pXlnA in YP medium induced by methanol. Molecular weight of the recombinant xylanase A was 35 kDa, that was consistent with the theoretical calculation and the enzyme activity in the culture was 7310 U/mL. Maximal xylanase activity (11180 U/mL) was gained after culturing the recombinant yeast for 120 hours in the present of 1% methanol. Among of seven media (BMMY, MMY, MM, YPM, YPTM, YPTCM, and YP) utilized for the yeast culture, the highest activity of the produced recombinant xylanase A (21620 U/mL) was reached in BMMY medium, while the lowest activity (1410 U/mL) was found in YPTCM medium. At the appropriate conditions, the recombinant xylanase A activity was 2.96 folds higher than that expressed in normal conditions. The conditions for recombinant xylanase A enzymatic hydrolysis of several agricultural wastes were also investigated. The results showed that in appropriate conditions (40oC, 24 hours, substrate concentration of 40 mg), the highest amount of reducing sugars produced from cob, rice bran and soybean meal substrates were 0.617 ± 0.002 μmol/mL, 0.663 ± 0.002 μmol/mL, and 0.814 ± 0.003 μmol/mL, respectively. Overall, with these distinctive properties, the recombinant xylanase A may initially become a potential candidate for various industrial applications.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"43 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76233348","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-26DOI: 10.15625/1811-4989/17650
Pham Thi Lan, Bui Van Cuong, Le Thi My Hanh, N. T. Phuong Lan, Kushnir Roman, Usacheva Tatyana
In recent years, the research and discovery of antioxidants of natural origin, such as those found plants, have increased dramatically. Ellagic acid is a bioactive compound found in many fruits and vegetables, which carries many biological activities, such as antioxidant, anti-inflammatory, anti-cancer and antibacterial activities. However, the low solubility of ellagic acid in water decreases its practical application. In this study, a complex of ellagic acid with hydroxypropyl-cyclodextrin was synthesized in the water-ethanol solvent. The results showed that the solvent with a volume content of EtOH of 20% was the most suitable for complex formation, with complexation yield of 46%. The complex was characterized by FTIR, DSC methods. The infrared spectrum of the complex is similar to that of HP-β-CD, however, the intensity and position of some oscillations in the complex have changed significantly, compared to spectra of EA and HP-β-CD. The sharp adsorbance band at 3475 cm-1 of the O-H bond of EA was not observed in the spectrum of the complex, indicating that the O-H group participated in the bonding and covered by the hollow cavity of the HP-β-CD molecules. The DSC curve of the complex shows that the melting points of EA and HPβCD in the complex are declined in terms of temperature and intensity. This is evidence that there is a complex interaction between EA and HPβCD. The complexation improved the solubility and antioxidant activity of EA. Especifically, the solubility of EA was increased by 3.2 times compared to raw EA; EC50 value of EA was reduced from 5.3x10-5 to 4.9x10-5mol. L-1 after complexation.
{"title":"Preparation of inclusion complex between ellagic acid and hydroxypropyl-β-cyclodextrin","authors":"Pham Thi Lan, Bui Van Cuong, Le Thi My Hanh, N. T. Phuong Lan, Kushnir Roman, Usacheva Tatyana","doi":"10.15625/1811-4989/17650","DOIUrl":"https://doi.org/10.15625/1811-4989/17650","url":null,"abstract":"In recent years, the research and discovery of antioxidants of natural origin, such as those found plants, have increased dramatically. Ellagic acid is a bioactive compound found in many fruits and vegetables, which carries many biological activities, such as antioxidant, anti-inflammatory, anti-cancer and antibacterial activities. However, the low solubility of ellagic acid in water decreases its practical application. In this study, a complex of ellagic acid with hydroxypropyl-cyclodextrin was synthesized in the water-ethanol solvent. The results showed that the solvent with a volume content of EtOH of 20% was the most suitable for complex formation, with complexation yield of 46%. The complex was characterized by FTIR, DSC methods. The infrared spectrum of the complex is similar to that of HP-β-CD, however, the intensity and position of some oscillations in the complex have changed significantly, compared to spectra of EA and HP-β-CD. The sharp adsorbance band at 3475 cm-1 of the O-H bond of EA was not observed in the spectrum of the complex, indicating that the O-H group participated in the bonding and covered by the hollow cavity of the HP-β-CD molecules. The DSC curve of the complex shows that the melting points of EA and HPβCD in the complex are declined in terms of temperature and intensity. This is evidence that there is a complex interaction between EA and HPβCD. The complexation improved the solubility and antioxidant activity of EA. Especifically, the solubility of EA was increased by 3.2 times compared to raw EA; EC50 value of EA was reduced from 5.3x10-5 to 4.9x10-5mol. L-1 after complexation.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"31 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82902942","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-08-26DOI: 10.15625/1811-4989/18018
Trinh Khanh Linh, Bui Van Ngoc
In this study, eukaryotic microbial communities associated with coral Acropora formosa and its natural surroundings, sediment and seawater, in a coral reef ecosystem of Whale Island, Nha Trang Bay, Vietnam were investigated. First, genetic material was taken from Acropora formosa’s surface mucus layer (SML) as well as the sediment underneath and seawater above the colonies from four different sampling locations in a coral reef ecosystem. Subsequently, the data were sequenced using 18S rRNA gene amplicon sequencing method. Sequences (reads) were then analyzed in Rstudio version 4.2.0. Bioinfomatic tools such as DADA2 pipeline clustered the sequences into amplicon sequence variants (ASVs), to which the taxonomy was assigned using SILVA 132 database. The majority of the sequences was categorized at the kingdom and phylum levels, but fewer sequences were identified at genus and species level. The visualization of the results revealed changes in abundance and composition of the eukaryotic communities in all samples. The results demonstrated that phylum Dinoflagellata had the highest relative abundance in coral samples. Meanwhile, Ochrophyta was the most prevalent phylum in seawater samples. Notably, after filtering out the sequences with abundance less than 2%, only genus Symbiodinium appeared significantly in coral samples. The composition of samples from coral sampling sites was more consistent. The same was true for samples of seawater, whereas the composition of sediment samples varied more. Alpha and beta diversity indices confirmed that there were significant differences (p < 0.05) in abundance and composition of eukaryotic communities among three different habitats. These findings come as the first effort to explore the diversity of eukaryotic communities in different habitats and could be valuable for further study in functional profiling or metabolic functions of microbial communities in the coral ecosystem.
{"title":"Comparative analysis of eukaryotic microbial communities associated with Acropora formosa, sediment, and seawater in a coral reef ecosystem of Whale island, Nha Trang bay, Vietnam","authors":"Trinh Khanh Linh, Bui Van Ngoc","doi":"10.15625/1811-4989/18018","DOIUrl":"https://doi.org/10.15625/1811-4989/18018","url":null,"abstract":"In this study, eukaryotic microbial communities associated with coral Acropora formosa and its natural surroundings, sediment and seawater, in a coral reef ecosystem of Whale Island, Nha Trang Bay, Vietnam were investigated. First, genetic material was taken from Acropora formosa’s surface mucus layer (SML) as well as the sediment underneath and seawater above the colonies from four different sampling locations in a coral reef ecosystem. Subsequently, the data were sequenced using 18S rRNA gene amplicon sequencing method. Sequences (reads) were then analyzed in Rstudio version 4.2.0. Bioinfomatic tools such as DADA2 pipeline clustered the sequences into amplicon sequence variants (ASVs), to which the taxonomy was assigned using SILVA 132 database. The majority of the sequences was categorized at the kingdom and phylum levels, but fewer sequences were identified at genus and species level. The visualization of the results revealed changes in abundance and composition of the eukaryotic communities in all samples. The results demonstrated that phylum Dinoflagellata had the highest relative abundance in coral samples. Meanwhile, Ochrophyta was the most prevalent phylum in seawater samples. Notably, after filtering out the sequences with abundance less than 2%, only genus Symbiodinium appeared significantly in coral samples. The composition of samples from coral sampling sites was more consistent. The same was true for samples of seawater, whereas the composition of sediment samples varied more. Alpha and beta diversity indices confirmed that there were significant differences (p < 0.05) in abundance and composition of eukaryotic communities among three different habitats. These findings come as the first effort to explore the diversity of eukaryotic communities in different habitats and could be valuable for further study in functional profiling or metabolic functions of microbial communities in the coral ecosystem.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"17 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72778748","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18629
Thi Van Anh Nguyen, Kieu-Oanh Nguyen Thi, Nhung Phuong Nguyen, H. Le
Distichochlamys citrea (DC) is an endemic ginger species used in treating associated-heart diseases in traditional medicine in Vietnam. However, scientific evidence to support the local use of this plant was limited. The present study aimed to investigate the antioxidant and antithrombotic activities of D. citrea extracts for the first time. The antioxidant activity of DC extracts was assessed by scavenging DPPH radical and measuring their total phenolic content (TPC). The antithrombotic activity was evaluated by inhibiting platelet aggregation and prolonging blood coagulation. Volatile components elucidated by GC-MS were docked with typical platelet receptors, including COX-1 and P2Y12. Results showed that the methanol extract of D. citrea exhibited a stronger DPPH scavenging ability (IC50 = 0.33 ± 0.00 mg/mL) and a higher TPC (8.09 ± 0.21%) than other extracts (p < 0.05). On the other hand, the hexane extract of D. citrea (DC-HX) had a remarkable inhibiting impact on ADP-, collagen- and ristocetin–induced platelet aggregation in a dose-dependent manner (Pearson’s correlation, r > 0.90, p < 0.05). In contrast, this extract did not lengthen the clotting time through any factors, such as PT (prothrombin time), and TT (thrombin time), except for APTT (activated partial thromboplastin time) at 4 mg/mL of the extract. GC-MS revealed that oxygenated hydrocarbons (54.45%) dominated the volatile profile of DC-HX, followed by sesquiterpens (37.18%) and diterpenes (6.66%). In the platelet aggregation process, several compounds in DC-HX were firmly bound to COX-1 and P2Y12, which might partly explain the significant antiaggregatory activity of this fraction. In conclusion, Distichochlamys citrea may be a potential source of active phytoconstituents for treating radicals- and cardiovascular-associated diseases.
{"title":"Antioxidant and antithrombotic activities of the Distichochlamys citrea leaves extract","authors":"Thi Van Anh Nguyen, Kieu-Oanh Nguyen Thi, Nhung Phuong Nguyen, H. Le","doi":"10.15625/1811-4989/18629","DOIUrl":"https://doi.org/10.15625/1811-4989/18629","url":null,"abstract":"Distichochlamys citrea (DC) is an endemic ginger species used in treating associated-heart diseases in traditional medicine in Vietnam. However, scientific evidence to support the local use of this plant was limited. The present study aimed to investigate the antioxidant and antithrombotic activities of D. citrea extracts for the first time. The antioxidant activity of DC extracts was assessed by scavenging DPPH radical and measuring their total phenolic content (TPC). The antithrombotic activity was evaluated by inhibiting platelet aggregation and prolonging blood coagulation. Volatile components elucidated by GC-MS were docked with typical platelet receptors, including COX-1 and P2Y12. Results showed that the methanol extract of D. citrea exhibited a stronger DPPH scavenging ability (IC50 = 0.33 ± 0.00 mg/mL) and a higher TPC (8.09 ± 0.21%) than other extracts (p < 0.05). On the other hand, the hexane extract of D. citrea (DC-HX) had a remarkable inhibiting impact on ADP-, collagen- and ristocetin–induced platelet aggregation in a dose-dependent manner (Pearson’s correlation, r > 0.90, p < 0.05). In contrast, this extract did not lengthen the clotting time through any factors, such as PT (prothrombin time), and TT (thrombin time), except for APTT (activated partial thromboplastin time) at 4 mg/mL of the extract. GC-MS revealed that oxygenated hydrocarbons (54.45%) dominated the volatile profile of DC-HX, followed by sesquiterpens (37.18%) and diterpenes (6.66%). In the platelet aggregation process, several compounds in DC-HX were firmly bound to COX-1 and P2Y12, which might partly explain the significant antiaggregatory activity of this fraction. In conclusion, Distichochlamys citrea may be a potential source of active phytoconstituents for treating radicals- and cardiovascular-associated diseases.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"113 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139366431","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18276
Q. Thai, Phuoc-Hai Huynh, Huyen Nguyen Thi Thuong, Quoc-Dang Quan
The COVID-19 pandemic is ongoing and spreading around the world, which means a continuous increase in the number of infections and death. SARS-CoV-2 constantly rapidly stored mutation in the Spike gene to adapt with the host cell. The Spike gene encoded spike protein directly interacts with hACE2 on the human cell surface. Herein, using the network centrality and molecular docking approaches, we detected key mutations that positively affect spike protein. Based on network centrality, we demonstrate that the A23403G (D614G) mutation in the Spike gene is the center of a network which means this mutation has a positive effect on the virus. In addition, analyzing the interaction of spike protein with hACE2, we highlighted that the mutation appeared in the RBD region by changing the electrostatic energy of the complex. Remarkably, mutations N440K, L452R, T478K, E484K, Q493R, and Q498R increased binding free energy of Spike-hACE2 complex due to the change of the side chain into a positive charge. The Eta, Delta, and Omicron variants existed in one or more of these mutations resulting in higher binding free energy and binding affinity than the Wuhan variant indicating sounder interaction with hACE2. In general, mutations appearing on the spike protein tended to cause the surface to become positively charged in order to interact easily with the negative surface of the hACE2 receptor.
{"title":"Investigating the impact of spike protein mutations on SARS-CoV-2 virulence in benin using network centrality and molecular docking approaches","authors":"Q. Thai, Phuoc-Hai Huynh, Huyen Nguyen Thi Thuong, Quoc-Dang Quan","doi":"10.15625/1811-4989/18276","DOIUrl":"https://doi.org/10.15625/1811-4989/18276","url":null,"abstract":"The COVID-19 pandemic is ongoing and spreading around the world, which means a continuous increase in the number of infections and death. SARS-CoV-2 constantly rapidly stored mutation in the Spike gene to adapt with the host cell. The Spike gene encoded spike protein directly interacts with hACE2 on the human cell surface. Herein, using the network centrality and molecular docking approaches, we detected key mutations that positively affect spike protein. Based on network centrality, we demonstrate that the A23403G (D614G) mutation in the Spike gene is the center of a network which means this mutation has a positive effect on the virus. In addition, analyzing the interaction of spike protein with hACE2, we highlighted that the mutation appeared in the RBD region by changing the electrostatic energy of the complex. Remarkably, mutations N440K, L452R, T478K, E484K, Q493R, and Q498R increased binding free energy of Spike-hACE2 complex due to the change of the side chain into a positive charge. The Eta, Delta, and Omicron variants existed in one or more of these mutations resulting in higher binding free energy and binding affinity than the Wuhan variant indicating sounder interaction with hACE2. In general, mutations appearing on the spike protein tended to cause the surface to become positively charged in order to interact easily with the negative surface of the hACE2 receptor.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"105 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85170359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18199
Thien-Hoang Ho, Uyen-Thanh Nguyen Thi, Quoc-Dang Quan, Kim-Tuyen Nguyen Thi, Trang H. D. Nguyen, Dinh-Thach Bui
Zika virus (ZIKV) belongs to the flavivirus family, and infection with ZIKV can lead to microcephaly, neurological issues like Guillain-Barré syndrome, and other birth defects. Zika virus can cause serious complications during pregnancy, such as delivery complications and pregnancy problems. It can also lead to severe illnesses, including swelling of the brain and spinal cord, as well as bleeding disorders. The Zika virus gained worldwide attention during the pandemic in Brazil, which led to extensive research efforts to discover effective and safe anti-Zika virus therapies. This study aimed to determine the efficacy of several bioactive compounds of plant origin against ZIKV NS5 RNA-dependent RNA polymerase (RdRp) (PDB ID: 5WZ3 and 5U04), ZIKV NS3 helicase (NS3h) (PDB ID: 5JRZ), Human tyrosine-protein kinase receptor UFO (Axl Receptor) (PDB ID: 2C5D), and human Axl Kinase (PDB ID: 5U6B). Fifty-three compounds from Eclipta prostrata (L.) were selected for screening based on the molecular docking method. The findings showed that these compounds inhibit ZIKV infection with high values of bond strength and free binding energy. AutoDock Vina results indicated that ecliptasaponin A exhibited the highest score value of -8.6 kcal/mol against the human Axl receptor, while eclalbasaponin I had the highest score value of -9.6 kcal/mol against ZIKV-NS2h. Additionally, echinocystic acid demonstrated the highest score value of -10.0 kcal/mol against ZIKV-NS5-RdRp (PDB: 5U04), while ursolic acid had the highest score of -9.9 kcal/mol against Axl kinase. Furthermore, it is noteworthy that ecliptasaponin, α-amyrin, ecliptasaponin A, and ursolic acid all had the highest score value of -9.9 kcal/mol against ZIKV-NS5-RdRp (PDB: 5WZ3). ADME prediction study found that echinocystic acid, eclalbasaponin I, and ecliptasaponin A have inhibitory abilities and are highly pharmacologically active, while α-amyrin and ursolic acid showed no results. However, all five substances are insoluble and lack optimal saturation, making oral absorption limited. These results in silico demonstrated that the bioactive compound from E. prostrata exhibited strong potential for developing inhibitory drugs against Zika virus.
{"title":"In silico screening for anti-Zika Virus compounds from Eclipta prostrata by molecular docking","authors":"Thien-Hoang Ho, Uyen-Thanh Nguyen Thi, Quoc-Dang Quan, Kim-Tuyen Nguyen Thi, Trang H. D. Nguyen, Dinh-Thach Bui","doi":"10.15625/1811-4989/18199","DOIUrl":"https://doi.org/10.15625/1811-4989/18199","url":null,"abstract":"Zika virus (ZIKV) belongs to the flavivirus family, and infection with ZIKV can lead to microcephaly, neurological issues like Guillain-Barré syndrome, and other birth defects. Zika virus can cause serious complications during pregnancy, such as delivery complications and pregnancy problems. It can also lead to severe illnesses, including swelling of the brain and spinal cord, as well as bleeding disorders. The Zika virus gained worldwide attention during the pandemic in Brazil, which led to extensive research efforts to discover effective and safe anti-Zika virus therapies. This study aimed to determine the efficacy of several bioactive compounds of plant origin against ZIKV NS5 RNA-dependent RNA polymerase (RdRp) (PDB ID: 5WZ3 and 5U04), ZIKV NS3 helicase (NS3h) (PDB ID: 5JRZ), Human tyrosine-protein kinase receptor UFO (Axl Receptor) (PDB ID: 2C5D), and human Axl Kinase (PDB ID: 5U6B). Fifty-three compounds from Eclipta prostrata (L.) were selected for screening based on the molecular docking method. The findings showed that these compounds inhibit ZIKV infection with high values of bond strength and free binding energy. AutoDock Vina results indicated that ecliptasaponin A exhibited the highest score value of -8.6 kcal/mol against the human Axl receptor, while eclalbasaponin I had the highest score value of -9.6 kcal/mol against ZIKV-NS2h. Additionally, echinocystic acid demonstrated the highest score value of -10.0 kcal/mol against ZIKV-NS5-RdRp (PDB: 5U04), while ursolic acid had the highest score of -9.9 kcal/mol against Axl kinase. Furthermore, it is noteworthy that ecliptasaponin, α-amyrin, ecliptasaponin A, and ursolic acid all had the highest score value of -9.9 kcal/mol against ZIKV-NS5-RdRp (PDB: 5WZ3). ADME prediction study found that echinocystic acid, eclalbasaponin I, and ecliptasaponin A have inhibitory abilities and are highly pharmacologically active, while α-amyrin and ursolic acid showed no results. However, all five substances are insoluble and lack optimal saturation, making oral absorption limited. These results in silico demonstrated that the bioactive compound from E. prostrata exhibited strong potential for developing inhibitory drugs against Zika virus.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139367298","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18201
Phan Thi Quy Quyen, Le Thi Van Anh, Ho Le Han, Tran Thi My Kieu, Tran Thi Ngoc Thu, Nguyen Thi Dong Phuong
Larvae live in soil have been well known for containing abundant microbiota in their gut. This study isolated six bacterial genera from the gut of larvae Protaetia brevitarsis seulensis including Bacillus, Cellulosimicrobium, Microbacterium, Streptomyces, Krasilnikoviella and Isoptericola based on specific media. Among these six genera, Cellulosimicrobium was collected for further analysis of cellulose-degrading features because of the most abundance and less studies up to now. Based on the 16S rDNA gene, the Cellulosimicrobium isolates were classified to C. cellulans, C. aquatile, C. funkei, C. protaetiae that were respectively isolated from four specific media such as modified ISP-2, MRS, modified anaerobic medium, modified fermentation medium. The analysis of their genome proved the presence of genes encoding for chitinases, alkyl resorcinol, and glucosidase in four strains. These cellulose degrading enzymes were useful for textile processing, paper recycling, production of nutritional supplements, food industry, production of alcohol from lignocellulosic materials, and beneficial microorganisms in denitrification and N-cycling in forest ecosystem as well as wastewater process.
{"title":"Isolation of cellulose-degrading cellulosimicrobium from larval gut of protaetia brevitarsis seulensis","authors":"Phan Thi Quy Quyen, Le Thi Van Anh, Ho Le Han, Tran Thi My Kieu, Tran Thi Ngoc Thu, Nguyen Thi Dong Phuong","doi":"10.15625/1811-4989/18201","DOIUrl":"https://doi.org/10.15625/1811-4989/18201","url":null,"abstract":"Larvae live in soil have been well known for containing abundant microbiota in their gut. This study isolated six bacterial genera from the gut of larvae Protaetia brevitarsis seulensis including Bacillus, Cellulosimicrobium, Microbacterium, Streptomyces, Krasilnikoviella and Isoptericola based on specific media. Among these six genera, Cellulosimicrobium was collected for further analysis of cellulose-degrading features because of the most abundance and less studies up to now. Based on the 16S rDNA gene, the Cellulosimicrobium isolates were classified to C. cellulans, C. aquatile, C. funkei, C. protaetiae that were respectively isolated from four specific media such as modified ISP-2, MRS, modified anaerobic medium, modified fermentation medium. The analysis of their genome proved the presence of genes encoding for chitinases, alkyl resorcinol, and glucosidase in four strains. These cellulose degrading enzymes were useful for textile processing, paper recycling, production of nutritional supplements, food industry, production of alcohol from lignocellulosic materials, and beneficial microorganisms in denitrification and N-cycling in forest ecosystem as well as wastewater process.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136368473","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18087
Nguyen Thi Sam, Nguyen Thi Huyen, Nguyen Thi Phuong Anh, Pham The Dan, Nguyen Thi Thuy Ngan, Chu Hoang Ha, Nguyen Trung Nam
Mesenchymal stem cells (MSCs) have become an effective tool for treating immune-related diseases due to their multilineage potential and immunomodulatory capabilities. However, a high cell dose is frequently essential for stem cell infusion in clinical practice. Therefore, it is necessary to produce sufficient quantities of MSCs while ensuring cell quality for clinical application in humans. To be able to use stem cells in patients requires a more rigorous captive procedure than using a xeno-free medium that does not contain substances derived from the hypothetical allergenic regime. Therefore, current cell culture procedures substitute xeno-free culture media with added supplement serum for the traditional DMEM media with bovine fetal serum (FBS). This switch increased the production cost immensely and made it difficult to produce MSCs on an industrial scale. In this study, we optimized the condition of MSCs’ cultures by adjusting the amount of the supplement serum usage to reduce production costs for industrial manufacturing. This is the first study to claim that reducing the amount of xeno-free supplement serum had no effect on the quality of hUC-MSCs isolated from Vietnamese children’s umbilical cords.
{"title":"Optimizing culture conditions of human umbilical cord mesenchymal stem cells (hUC-MSCs) by adjusting the volume of xeno-free supplement serum","authors":"Nguyen Thi Sam, Nguyen Thi Huyen, Nguyen Thi Phuong Anh, Pham The Dan, Nguyen Thi Thuy Ngan, Chu Hoang Ha, Nguyen Trung Nam","doi":"10.15625/1811-4989/18087","DOIUrl":"https://doi.org/10.15625/1811-4989/18087","url":null,"abstract":"Mesenchymal stem cells (MSCs) have become an effective tool for treating immune-related diseases due to their multilineage potential and immunomodulatory capabilities. However, a high cell dose is frequently essential for stem cell infusion in clinical practice. Therefore, it is necessary to produce sufficient quantities of MSCs while ensuring cell quality for clinical application in humans. To be able to use stem cells in patients requires a more rigorous captive procedure than using a xeno-free medium that does not contain substances derived from the hypothetical allergenic regime. Therefore, current cell culture procedures substitute xeno-free culture media with added supplement serum for the traditional DMEM media with bovine fetal serum (FBS). This switch increased the production cost immensely and made it difficult to produce MSCs on an industrial scale. In this study, we optimized the condition of MSCs’ cultures by adjusting the amount of the supplement serum usage to reduce production costs for industrial manufacturing. This is the first study to claim that reducing the amount of xeno-free supplement serum had no effect on the quality of hUC-MSCs isolated from Vietnamese children’s umbilical cords.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136368875","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18240
Trang Thi Huyen Tran, Binh Thi Nguyen Le, Sang Van Nguyen, Oanh Thi Phuong Kim
Insulin-like growth factor binding protein-3 (IGFBP-3) has an important role on the growth of teleost fish. The association between genetic variations of IGFBP-3 gene and the growth of striped catfish, Pangasianodon hypophthalmus, was investigated in this study. To discover SNPs, fragments of IGFBP-3 gene from 10 fast-growing fish and 10 slow-growing fish were directly sequenced. Among 10 putative SNPs, a non-synonymous SNP 704 C>G (p.Leu8Val) located at coding region of exon 1 was filtered and subjected to validate in 70 fast-growing fish and 70 slow–growing fish by individual genotyping. Our statistical analysis showed the significant association between SNP 704 C>G (p.Leu8Val) and growth traits of striped catfish (p < 0.01). The genetic diversity of the SNP was evaluated by polymorphism content (PIC) and minor allele frequency (MAF). These values indicated that this SNP was common variant with moderate genetic diversity. The non-synonymous SNP 704 C>G (p.Leu8Val) in IGFBP-3 gene is a potential candidate for subsequent development of molecular marker for growth traits in breeding of the striped catfish.
{"title":"Non-synonymous polymorphism in IGFBP-3 gene associated with growth traits in striped catfish (Pangasianodon hypophthalmus, Sauvage, 1878)","authors":"Trang Thi Huyen Tran, Binh Thi Nguyen Le, Sang Van Nguyen, Oanh Thi Phuong Kim","doi":"10.15625/1811-4989/18240","DOIUrl":"https://doi.org/10.15625/1811-4989/18240","url":null,"abstract":"Insulin-like growth factor binding protein-3 (IGFBP-3) has an important role on the growth of teleost fish. The association between genetic variations of IGFBP-3 gene and the growth of striped catfish, Pangasianodon hypophthalmus, was investigated in this study. To discover SNPs, fragments of IGFBP-3 gene from 10 fast-growing fish and 10 slow-growing fish were directly sequenced. Among 10 putative SNPs, a non-synonymous SNP 704 C>G (p.Leu8Val) located at coding region of exon 1 was filtered and subjected to validate in 70 fast-growing fish and 70 slow–growing fish by individual genotyping. Our statistical analysis showed the significant association between SNP 704 C>G (p.Leu8Val) and growth traits of striped catfish (p < 0.01). The genetic diversity of the SNP was evaluated by polymorphism content (PIC) and minor allele frequency (MAF). These values indicated that this SNP was common variant with moderate genetic diversity. The non-synonymous SNP 704 C>G (p.Leu8Val) in IGFBP-3 gene is a potential candidate for subsequent development of molecular marker for growth traits in breeding of the striped catfish.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136369848","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-06-30DOI: 10.15625/1811-4989/18177
Doan Thi Thanh Huong, Nguyen Thi Thu Hien, Do Thi Roan, Luu Minh Duc, Le Thi Hue, Le Thanh Hoa, Le Thi Kim Xuyen, Nguyen Thi Khue
Marek’s disease is a contagious avian viral disease that is caused by a Marek’s disease virus serotype 1 (MDV-1) or gallid herpesvirus 2 (GaHV-2), a member of the genus Alphaherpesvirus, family Herpesviridae. Up to now, the disease has caused significant losses to the chicken farming industry in many provinces and cities across the country. In this study, four MDV-1 (GaHV-2) strains causing the disease in Bac Ninh province during the 2019–2022 period were identified by multiplex Polymerase Chain Reaction (PCR). Subsequently, the segments of 1020 bp encoding 339 amino acids of Meq gene (Marek’s disease virus EcoRI fragment Q) from four samples were collected and sequenced. The rate of identity and homology between the four Vietnamese strains and other global strains ranged from 89.4% to 100% and 87.6% to 100%, respectively. These rates were higher between the four Vietnamese strains and MDV-1 Chinese strains, ranging from 99.2% to 100% and 98.2% to 100%, respectively. The molecular characterization of the Meq gene revealed that all four of the GaHV-2 strains infecting chickens in the Bac Ninh province belonged to the highly virulent group, with a low proline ratio in Meq protein (ranging from 20.59–21.18%), consisting of three PPPP motifs and three interrupted motifs that contain mutations at the second position of the proline rich region (PRR): PPPP>P (Q/A/R)PP. Overall, this study provides valuable information on molecular characteristics of MDV-1 strains in Bac Ninh province during the 2019–2022 period.
{"title":"Sequencing and analysis of the Meq oncogene of MDV causing marek’s disease in Bac Ninh province from 2019 to 2022","authors":"Doan Thi Thanh Huong, Nguyen Thi Thu Hien, Do Thi Roan, Luu Minh Duc, Le Thi Hue, Le Thanh Hoa, Le Thi Kim Xuyen, Nguyen Thi Khue","doi":"10.15625/1811-4989/18177","DOIUrl":"https://doi.org/10.15625/1811-4989/18177","url":null,"abstract":"Marek’s disease is a contagious avian viral disease that is caused by a Marek’s disease virus serotype 1 (MDV-1) or gallid herpesvirus 2 (GaHV-2), a member of the genus Alphaherpesvirus, family Herpesviridae. Up to now, the disease has caused significant losses to the chicken farming industry in many provinces and cities across the country. In this study, four MDV-1 (GaHV-2) strains causing the disease in Bac Ninh province during the 2019–2022 period were identified by multiplex Polymerase Chain Reaction (PCR). Subsequently, the segments of 1020 bp encoding 339 amino acids of Meq gene (Marek’s disease virus EcoRI fragment Q) from four samples were collected and sequenced. The rate of identity and homology between the four Vietnamese strains and other global strains ranged from 89.4% to 100% and 87.6% to 100%, respectively. These rates were higher between the four Vietnamese strains and MDV-1 Chinese strains, ranging from 99.2% to 100% and 98.2% to 100%, respectively. The molecular characterization of the Meq gene revealed that all four of the GaHV-2 strains infecting chickens in the Bac Ninh province belonged to the highly virulent group, with a low proline ratio in Meq protein (ranging from 20.59–21.18%), consisting of three PPPP motifs and three interrupted motifs that contain mutations at the second position of the proline rich region (PRR): PPPP>P (Q/A/R)PP. Overall, this study provides valuable information on molecular characteristics of MDV-1 strains in Bac Ninh province during the 2019–2022 period.","PeriodicalId":23622,"journal":{"name":"Vietnam Journal of Biotechnology","volume":"42 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136369849","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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