Pub Date : 2021-12-31DOI: 10.22146/ijbiotech.65989
Wahyu Aristyaning Putri, Hanum Mukti Rahayu, A. Khasanah, L. Sembiring, M. Kawaichi, Y. A. Purwestri
Streptomyces is one of mercury‐resistant bacteria which can convert Hg2+ into nontoxic Hg0 . This study aimed to identify mercury‐resistant Streptomyces present in the Cyperus rotundus rhizosphere from artisanal small‐scale gold mining (ASGM) area and clone merA gene to the cloning and expression vectors. Molecular identification was conducted using 16s rRNA gene with the maximum likelihood algorithms. Results revealed that the AS1 and AS2 strains were a group of Streptomyces ardesiacus and the BR28 strain was closed to Brevibacillus agri. The AS2 merA gene was cloned to pMD20 cloning vectors, pGEX‐5x‐1 and pET‐28c expression vectors. The transformation was successfully performed in BL21 and DH5α competent cells. The full length of the merA gene was confirmed to be 1,425 bp. This study is the first research on identifying mercury‐resistant Streptomyces and cloning the full‐length merA gene in Indonesia.
{"title":"Identification of mercury‐resistant Streptomyces isolated from Cyperus rotundus L. rhizosphere and molecular cloning of mercury (II) reductase gene","authors":"Wahyu Aristyaning Putri, Hanum Mukti Rahayu, A. Khasanah, L. Sembiring, M. Kawaichi, Y. A. Purwestri","doi":"10.22146/ijbiotech.65989","DOIUrl":"https://doi.org/10.22146/ijbiotech.65989","url":null,"abstract":"Streptomyces is one of mercury‐resistant bacteria which can convert Hg2+ into nontoxic Hg0 . This study aimed to identify mercury‐resistant Streptomyces present in the Cyperus rotundus rhizosphere from artisanal small‐scale gold mining (ASGM) area and clone merA gene to the cloning and expression vectors. Molecular identification was conducted using 16s rRNA gene with the maximum likelihood algorithms. Results revealed that the AS1 and AS2 strains were a group of Streptomyces ardesiacus and the BR28 strain was closed to Brevibacillus agri. The AS2 merA gene was cloned to pMD20 cloning vectors, pGEX‐5x‐1 and pET‐28c expression vectors. The transformation was successfully performed in BL21 and DH5α competent cells. The full length of the merA gene was confirmed to be 1,425 bp. This study is the first research on identifying mercury‐resistant Streptomyces and cloning the full‐length merA gene in Indonesia.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49094247","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 : 2021-12-31DOI: 10.22146/ijbiotech.64472
Gita Dwi Prasasty, Miftahurrizqiyah Miftahurrizqiyah, C. Anwar, Dwi Handayani, Dalilah Dalilah, A. Ghiffari, Inda Astri Aryani, N. D. Lastuti, Afiat Berbudi
Scabies is a global disease with a high prevalence, causing morbidity and even mortality, especially in poor and developing countries. However, it is often misdiagnosed due to varied and unspecified lesions. The gold standard technique for diagnosis is a microscopic examination, which requires experienced experts in finding mites, mainly in ordinary scabies. CO1 and ITS2 genes have been widely used in molecular identification to detect Sarcoptes scabiei and its variants. This study aimed to determine and compare the sensitivity and specificity of CO1 and ITS2 S. scabiei genes to the microscopic examination of scabies skin scrapings. The skin scrapings of 52 subjects with scabies diagnosed by anamnesis, physical examination, and dermoscopic examination were examined under a microscope and analyzed by nested PCR. The diagnostic test result showed that the sensitivity of nested PCR of both CO1 and ITS2 genes to micro‐ scope examination was 100%. However, the specificity of both CO1 and ITS2 nested PCR was poor (24% and 0%). Hence, CO1 and ITS2 nested PCR could be more suitable for screening ordinary scabies in humans than the microscopic examination.
{"title":"Performance of CO1 and ITS2 nested PCR in molecular identification of ordinary scabies (Sarcoptes scabiei var. hominis)","authors":"Gita Dwi Prasasty, Miftahurrizqiyah Miftahurrizqiyah, C. Anwar, Dwi Handayani, Dalilah Dalilah, A. Ghiffari, Inda Astri Aryani, N. D. Lastuti, Afiat Berbudi","doi":"10.22146/ijbiotech.64472","DOIUrl":"https://doi.org/10.22146/ijbiotech.64472","url":null,"abstract":"Scabies is a global disease with a high prevalence, causing morbidity and even mortality, especially in poor and developing countries. However, it is often misdiagnosed due to varied and unspecified lesions. The gold standard technique for diagnosis is a microscopic examination, which requires experienced experts in finding mites, mainly in ordinary scabies. CO1 and ITS2 genes have been widely used in molecular identification to detect Sarcoptes scabiei and its variants. This study aimed to determine and compare the sensitivity and specificity of CO1 and ITS2 S. scabiei genes to the microscopic examination of scabies skin scrapings. The skin scrapings of 52 subjects with scabies diagnosed by anamnesis, physical examination, and dermoscopic examination were examined under a microscope and analyzed by nested PCR. The diagnostic test result showed that the sensitivity of nested PCR of both CO1 and ITS2 genes to micro‐ scope examination was 100%. However, the specificity of both CO1 and ITS2 nested PCR was poor (24% and 0%). Hence, CO1 and ITS2 nested PCR could be more suitable for screening ordinary scabies in humans than the microscopic examination.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45526844","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 : 2021-12-31DOI: 10.22146/ijbiotech.61425
Achmad Rodiansyah, S. Prabaningtyas, M. Ulfah, Ainul Fitria Mahmuda, Uun Rohmawati
Amylolytic bacteria are a source of amylase, which is an essential enzyme to support microalgae growth in the bioreactor for microalgae culture. In a previous study, the highest bacterial isolate to hydrolyze amylum (namely PAS) was successfully isolated from Ranu Pani, Indonesia, and it was identified as Bacillus amyloliquefaciens. That bacterial isolate (B. amyloliquefaciens PAS) also has been proven to accelerate Chlorella vulgaris growth in the mini bioreactor. This study aims to detect, isolate, and characterize the PAS’s α‐amylase encoding gene. This study was conducted with DNA extraction, amplification of α‐amylase gene with polymerase chain reaction (PCR) method with the specific primers, DNA sequencing, phylogenetic tree construction, and protein modeling. The result showed that α‐amylase was successfully detected in PAS bacterial isolate. The α‐amylase DNA fragment was obtained 1,468 bp and that translated sequence has an identity of about 98.3% compared to the B. amylolyquefaciens α‐amylase 3BH4 in the Protein Data Bank (PDB). The predicted 3D protein model of the PAS’s α‐amylase encoding gene has amino acid variations that predicted affect the protein’s structure in the small region. This research will be useful for further research to produce recombinant α‐amylase.
{"title":"Isolation and characterization of α ‐amylase encoding gene in Bacillus amyloliquefaciens PAS","authors":"Achmad Rodiansyah, S. Prabaningtyas, M. Ulfah, Ainul Fitria Mahmuda, Uun Rohmawati","doi":"10.22146/ijbiotech.61425","DOIUrl":"https://doi.org/10.22146/ijbiotech.61425","url":null,"abstract":"Amylolytic bacteria are a source of amylase, which is an essential enzyme to support microalgae growth in the bioreactor for microalgae culture. In a previous study, the highest bacterial isolate to hydrolyze amylum (namely PAS) was successfully isolated from Ranu Pani, Indonesia, and it was identified as Bacillus amyloliquefaciens. That bacterial isolate (B. amyloliquefaciens PAS) also has been proven to accelerate Chlorella vulgaris growth in the mini bioreactor. This study aims to detect, isolate, and characterize the PAS’s α‐amylase encoding gene. This study was conducted with DNA extraction, amplification of α‐amylase gene with polymerase chain reaction (PCR) method with the specific primers, DNA sequencing, phylogenetic tree construction, and protein modeling. The result showed that α‐amylase was successfully detected in PAS bacterial isolate. The α‐amylase DNA fragment was obtained 1,468 bp and that translated sequence has an identity of about 98.3% compared to the B. amylolyquefaciens α‐amylase 3BH4 in the Protein Data Bank (PDB). The predicted 3D protein model of the PAS’s α‐amylase encoding gene has amino acid variations that predicted affect the protein’s structure in the small region. This research will be useful for further research to produce recombinant α‐amylase.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45421437","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 : 2021-12-31DOI: 10.22146/ijbiotech.65142
Erdianty Setiabudi, K. Meitha, F. Dwivany
Banana is one of the most important commodities for maintaining global food security. Primary metabolic processes during the ripening of banana greatly affect post‐harvest quality, particularly in starch metabolism. The beta‐ amylase (BAM) gene family is known as a group of genes that plays an important role in starch metabolism regulation. In this study, we focused on the characterization and comparative analysis of the BAM gene family in DH Pahang and Pisang Klutuk Wulung (PKW) varieties, these being the AA and BB genomes, respectively. The sequences of BAM gene family were retrieved from the database of Musa acuminata ’DH Pahang’ and Musa balbisiana ’PKW’ genome, then structural and functional characterization was performed, followed by identification of cis‐acting elements in the BAM promoter regions. The results showed that the BAM gene family structure was relatively conserved in both genomes, and a putative BAM11 gene was found, the function of which has not been studied in other plants. Cis‐acting element analysis showed that they were distinct in the copy number and types of elements that were responsive to various phytohormones. This study suggested that the BAM genes involved in ripening are spatiotemporally regulated. However, further functional genomic analysis is required to describe the specific role and regulation of BAM genes during ripening in banana.
{"title":"In silico characterization and comparison of the fruit ripening related beta‐ amylase (BAM) gene family in banana genome A and B","authors":"Erdianty Setiabudi, K. Meitha, F. Dwivany","doi":"10.22146/ijbiotech.65142","DOIUrl":"https://doi.org/10.22146/ijbiotech.65142","url":null,"abstract":"Banana is one of the most important commodities for maintaining global food security. Primary metabolic processes during the ripening of banana greatly affect post‐harvest quality, particularly in starch metabolism. The beta‐ amylase (BAM) gene family is known as a group of genes that plays an important role in starch metabolism regulation. In this study, we focused on the characterization and comparative analysis of the BAM gene family in DH Pahang and Pisang Klutuk Wulung (PKW) varieties, these being the AA and BB genomes, respectively. The sequences of BAM gene family were retrieved from the database of Musa acuminata ’DH Pahang’ and Musa balbisiana ’PKW’ genome, then structural and functional characterization was performed, followed by identification of cis‐acting elements in the BAM promoter regions. The results showed that the BAM gene family structure was relatively conserved in both genomes, and a putative BAM11 gene was found, the function of which has not been studied in other plants. Cis‐acting element analysis showed that they were distinct in the copy number and types of elements that were responsive to various phytohormones. This study suggested that the BAM genes involved in ripening are spatiotemporally regulated. However, further functional genomic analysis is required to describe the specific role and regulation of BAM genes during ripening in banana.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42718901","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 : 2021-12-31DOI: 10.22146/ijbiotech.64893
Charlie Ester De Fretes, D. Widianto, Y. A. Purwestri, T. R. Nuringtyas
Application of high levels of chemical fertilizers for optimal growth of sweet sorghum causes environmental degradation. Plant growth‐promoting bacteria have biotechnological importance because they can improve the growth and health of important agronomic plants. This study aimed to isolate, characterize, and identify endophytic bacteria associated with sweet sorghum (cv. KCS105), and also to study the inoculation effects of selected isolates on sorghum growth. In this study, 35 isolates were evaluated for their ability to support plant growth. The results showed that seven isolates were diazotrophic, six were capable of dissolving phosphate, six produced IAA and could detect ACC‐deaminase activity, and three inhibited the growth of pathogenic fungi. Nine isolates exhibiting mechanisms for promoting plant growth from the Alphaproteobacteria (Devosia), Firmicutes (Bacillus, Paenibacillus, Staphylococcus), and Actinobacteria (Microbacterium, Brachybacterium) phyla were identified. In addition, the Paenibacillus sp. BB7, Bacillus sp. PIB1B, and Bacillus sp. PLB1B isolates showed increasing effects on plant growth in greenhouse tests. Endophytic bacterial isolates which display plant growth‐promoting features can potentially be employed as biofertilizer agents. They may also address environmental damage problems resulting from the use of chemical fertilizers and pesticides.
{"title":"Plant growth‐promoting activity of endophytic bacteria from sweet sorghum (Sorghum bicolor (L.) Moench)","authors":"Charlie Ester De Fretes, D. Widianto, Y. A. Purwestri, T. R. Nuringtyas","doi":"10.22146/ijbiotech.64893","DOIUrl":"https://doi.org/10.22146/ijbiotech.64893","url":null,"abstract":"Application of high levels of chemical fertilizers for optimal growth of sweet sorghum causes environmental degradation. Plant growth‐promoting bacteria have biotechnological importance because they can improve the growth and health of important agronomic plants. This study aimed to isolate, characterize, and identify endophytic bacteria associated with sweet sorghum (cv. KCS105), and also to study the inoculation effects of selected isolates on sorghum growth. In this study, 35 isolates were evaluated for their ability to support plant growth. The results showed that seven isolates were diazotrophic, six were capable of dissolving phosphate, six produced IAA and could detect ACC‐deaminase activity, and three inhibited the growth of pathogenic fungi. Nine isolates exhibiting mechanisms for promoting plant growth from the Alphaproteobacteria (Devosia), Firmicutes (Bacillus, Paenibacillus, Staphylococcus), and Actinobacteria (Microbacterium, Brachybacterium) phyla were identified. In addition, the Paenibacillus sp. BB7, Bacillus sp. PIB1B, and Bacillus sp. PLB1B isolates showed increasing effects on plant growth in greenhouse tests. Endophytic bacterial isolates which display plant growth‐promoting features can potentially be employed as biofertilizer agents. They may also address environmental damage problems resulting from the use of chemical fertilizers and pesticides.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41660500","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}
Proteases are enzymes used in industries such the production and processing of detergents, food, leather, and silk. The aim of this study was to isolate and identify protease‐producing bacteria from a sludge disposal site and from sediments. Soil samples were collected separately from the selected area. Samples weighing 1 g were serially diluted and spread onto skim milk agar. A total of 16 bacteria species were isolated from the study samples. Four bacterial isolates showed high proteolytic activity and were selected for enzymatic study based on their zone of proteolysis. The isolates were identified based on biochemical tests. The results indicated that the isolated bacteria were E. coli (99.69%), Pseudomonas putrefaciens (Shewanella putrefaciens) (91.61%), Bacillus carboniphilus (92.78%), and Lysinibacillus sphaericus (98.4%). The crude protease enzymes produced by these bacterial isolates showed promising results for application in dehairing and destaining as detergent additives. Bacillus carboniphilus showed the best level of activity and was selected as the most potent protease‐producing bacteria for both dehairing and destaining ability. Soils from sludge disposal sites and sediments from around tannery wastes could be good sources from which to isolate alkaline protease‐producing bacteria.
{"title":"Isolation and identification of protease‐producing bacteria from sludge and sediment soil around Adama, Ethiopia","authors":"Yeshaneh Adimasu Lemenh, T. Biru, Adinew Zewdu Chernet, Feleke Belachew Lema","doi":"10.22146/ijbiotech.63987","DOIUrl":"https://doi.org/10.22146/ijbiotech.63987","url":null,"abstract":"Proteases are enzymes used in industries such the production and processing of detergents, food, leather, and silk. The aim of this study was to isolate and identify protease‐producing bacteria from a sludge disposal site and from sediments. Soil samples were collected separately from the selected area. Samples weighing 1 g were serially diluted and spread onto skim milk agar. A total of 16 bacteria species were isolated from the study samples. Four bacterial isolates showed high proteolytic activity and were selected for enzymatic study based on their zone of proteolysis. The isolates were identified based on biochemical tests. The results indicated that the isolated bacteria were E. coli (99.69%), Pseudomonas putrefaciens (Shewanella putrefaciens) (91.61%), Bacillus carboniphilus (92.78%), and Lysinibacillus sphaericus (98.4%). The crude protease enzymes produced by these bacterial isolates showed promising results for application in dehairing and destaining as detergent additives. Bacillus carboniphilus showed the best level of activity and was selected as the most potent protease‐producing bacteria for both dehairing and destaining ability. Soils from sludge disposal sites and sediments from around tannery wastes could be good sources from which to isolate alkaline protease‐producing bacteria.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-12-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48511826","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 : 2021-09-30DOI: 10.22146/ijbiotech.65239
A. Utami, Pamela Apriliana, Yudi Kusnadi, D. S. Zilda, Z. Ilmiah, P. Lisdiyanti, S. Setyahadi, A. Uria
We investigated the biosynthetic potential of soil-associated actinobacteria originating from Indonesia, identified as Streptomyces luridus and as Streptomyces luteosporeus. Antimicrobial assays indicated inhibitory activity by both strains against the pathogen Pseudomonas aeruginosa, with S. luteosporeus particularly inhibiting the growth of Bacillus subtilis. PCR-amplification, cloning, and sequencing of ketosynthase (KS) domains of type I modular polyketide (PKS-I) and adenylation (AD) domains of non-ribosomal peptide synthetase (NRPS) indicated the diversity of KS and AD domains derived from both Indonesian Streptomyces. Further phylogenetic analysis showed that KS domains from the subclass cis-AT PKS can be classified as being a part of a loading module or an extension module, along with their predicted substrate specificity. The results suggest that both strains are a potential source of novel biosynthetic pathways. This genetic analysis approach can be used as a fast guide to obtain insight into natural product biosynthetic gene diversity in microorganisms.
{"title":"Analyzing the biosynthetic potential of antimicrobial-producing actinobacteria originating from Indonesia","authors":"A. Utami, Pamela Apriliana, Yudi Kusnadi, D. S. Zilda, Z. Ilmiah, P. Lisdiyanti, S. Setyahadi, A. Uria","doi":"10.22146/ijbiotech.65239","DOIUrl":"https://doi.org/10.22146/ijbiotech.65239","url":null,"abstract":"We investigated the biosynthetic potential of soil-associated actinobacteria originating from Indonesia, identified as Streptomyces luridus and as Streptomyces luteosporeus. Antimicrobial assays indicated inhibitory activity by both strains against the pathogen Pseudomonas aeruginosa, with S. luteosporeus particularly inhibiting the growth of Bacillus subtilis. PCR-amplification, cloning, and sequencing of ketosynthase (KS) domains of type I modular polyketide (PKS-I) and adenylation (AD) domains of non-ribosomal peptide synthetase (NRPS) indicated the diversity of KS and AD domains derived from both Indonesian Streptomyces. Further phylogenetic analysis showed that KS domains from the subclass cis-AT PKS can be classified as being a part of a loading module or an extension module, along with their predicted substrate specificity. The results suggest that both strains are a potential source of novel biosynthetic pathways. This genetic analysis approach can be used as a fast guide to obtain insight into natural product biosynthetic gene diversity in microorganisms.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41746273","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 : 2021-06-28DOI: 10.22146/ijbiotech.63318
Romaniyanto Romaniyanto, C. Prakoeswa, D. Tinduh, H. Notobroto, F. Rantam, D. Utomo, H. Suroto, F. Ferdiansyah
Low back pain is a crucial public health problem that is commonly associated with intervertebral disc de‐ generation and has vast socio‐economic impact worldwide. Current treatments for disc degeneration are conservative, non‐surgical, or surgical interventions, and there is no current clinical therapy aimed at directly reversing the degeneration. Given the limited capacity of intervertebral disc (IVD) cells to self‐repair, treatment aiming to regenerate IVDs is a topic of interest and mesenchymal stem cells (MSCs) have been identified as having potential in this regeneration. Recent studies have revealed that the benefits of MSC therapy could result from the molecules the cells secrete and that play principal roles in regulating essential biologic processes, rather than from the implanted cells themselves. Therefore, the objective of this study is to review the potential use of the MSC secretome to regenerate IVDs. Current evidence shows that the secretome may regenerate IVDs by modulating the gene expressions of nucleus pulposus cells (upregulation of keratin 19 and downregulation of matrix metalloproteinase 12 and matrix Gla protein) and stimulating IVD progenitor cells to repair the degenerated disc.
{"title":"The potential of mesenchymal stem‐cell secretome for regeneration of intervertebral disc: A review article","authors":"Romaniyanto Romaniyanto, C. Prakoeswa, D. Tinduh, H. Notobroto, F. Rantam, D. Utomo, H. Suroto, F. Ferdiansyah","doi":"10.22146/ijbiotech.63318","DOIUrl":"https://doi.org/10.22146/ijbiotech.63318","url":null,"abstract":"Low back pain is a crucial public health problem that is commonly associated with intervertebral disc de‐ generation and has vast socio‐economic impact worldwide. Current treatments for disc degeneration are conservative, non‐surgical, or surgical interventions, and there is no current clinical therapy aimed at directly reversing the degeneration. Given the limited capacity of intervertebral disc (IVD) cells to self‐repair, treatment aiming to regenerate IVDs is a topic of interest and mesenchymal stem cells (MSCs) have been identified as having potential in this regeneration. Recent studies have revealed that the benefits of MSC therapy could result from the molecules the cells secrete and that play principal roles in regulating essential biologic processes, rather than from the implanted cells themselves. Therefore, the objective of this study is to review the potential use of the MSC secretome to regenerate IVDs. Current evidence shows that the secretome may regenerate IVDs by modulating the gene expressions of nucleus pulposus cells (upregulation of keratin 19 and downregulation of matrix metalloproteinase 12 and matrix Gla protein) and stimulating IVD progenitor cells to repair the degenerated disc.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"46255349","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 : 2021-06-28DOI: 10.22146/ijbiotech.63260
D. Perwitasari, R. Maliza, B. Murti, H. Dania, Athika Darumas Putri
The World Health Organization (WHO) has announced that Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) and Coronavirus disease (COVID‐19) is considered a worldwide pandemic. Rapidly rising numbers of patients have been reported in almost every country, along with the growing mortality rates. Uncontrolled growth in patient numbers may be due to reasons such as treatment options and vaccine availabilities and unidentified targets of SARS‐CoV‐2. Previous study has revealed that the molecular target of SARS‐CoV‐2 is analogous to SARS (2003), i.e. angiotensin‐converting enzyme‐2 (ACE‐2). Therefore, the determination of ACE‐2 may enrich existing information and facilitate development of drugs targeted toward SARS‐CoV‐2. This study aims to screen the expression of ACE‐2 genes and their relationship to the types of SNP variants in SARS‐CoV‐2. We explored a series of observations using powerful databases, e.g. GTEx portal, HaploReg, 1000 Genome and Ensembl, to identify the gene variant of ACE‐2. We showed that ACE‐2 is highly expressed in the testes and small intestine, while its lowest level is observed in lymphocytes. Subsequently, we observed 17 gene variants containing a missense mutation potentially damaging protein level. Among these genes, single nucleotide polymorphism (SNP) rs370187012 shows the highest damage‐level score, while the lowest effect is in SNP rs4646116. The highest frequency of the C allele was observed in European populations (1%). In addition to showing that ACE‐2 is expressed in several organs, we concluded that the ACE‐2 gene variation can be found in African, American, Southeast and East Asian, and European populations. The polymorphisms of ACE‐2 impact on the ACE2 protein structure and the binding capacity of the ACE‐2 receptor with the S‐Protein of SARS‐CoV‐2.
{"title":"Identification of gene expression location of angiotensin‐converting enzyme‐2 SNPs as a receptor for SARS‐CoV‐2 in different populations by using various databases","authors":"D. Perwitasari, R. Maliza, B. Murti, H. Dania, Athika Darumas Putri","doi":"10.22146/ijbiotech.63260","DOIUrl":"https://doi.org/10.22146/ijbiotech.63260","url":null,"abstract":"The World Health Organization (WHO) has announced that Severe Acute Respiratory Syndrome Coronavirus‐2 (SARS‐CoV‐2) and Coronavirus disease (COVID‐19) is considered a worldwide pandemic. Rapidly rising numbers of patients have been reported in almost every country, along with the growing mortality rates. Uncontrolled growth in patient numbers may be due to reasons such as treatment options and vaccine availabilities and unidentified targets of SARS‐CoV‐2. Previous study has revealed that the molecular target of SARS‐CoV‐2 is analogous to SARS (2003), i.e. angiotensin‐converting enzyme‐2 (ACE‐2). Therefore, the determination of ACE‐2 may enrich existing information and facilitate development of drugs targeted toward SARS‐CoV‐2. This study aims to screen the expression of ACE‐2 genes and their relationship to the types of SNP variants in SARS‐CoV‐2. We explored a series of observations using powerful databases, e.g. GTEx portal, HaploReg, 1000 Genome and Ensembl, to identify the gene variant of ACE‐2. We showed that ACE‐2 is highly expressed in the testes and small intestine, while its lowest level is observed in lymphocytes. Subsequently, we observed 17 gene variants containing a missense mutation potentially damaging protein level. Among these genes, single nucleotide polymorphism (SNP) rs370187012 shows the highest damage‐level score, while the lowest effect is in SNP rs4646116. The highest frequency of the C allele was observed in European populations (1%). In addition to showing that ACE‐2 is expressed in several organs, we concluded that the ACE‐2 gene variation can be found in African, American, Southeast and East Asian, and European populations. The polymorphisms of ACE‐2 impact on the ACE2 protein structure and the binding capacity of the ACE‐2 receptor with the S‐Protein of SARS‐CoV‐2.","PeriodicalId":13452,"journal":{"name":"Indonesian Journal of Biotechnology","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2021-06-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49361031","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 : 2021-03-30DOI: 10.22146/IJBIOTECH.60174
J. A. N. Halim, S. N. Halim, Dionisius Denis, S. Haryanto, E. Dharmana, Rebriarina Hapsari, R. T. Sasmono, B. Yohan
Dengue virus (DENV) is the most geographically widespread arbovirus causing dengue disease epidemics in tropical and subtropical regions. Nature provides abundant plants as a source for lead molecules against various diseases including DENV infection. We investigated the antiviral effect of curcumin and 6‐gingerol, the major active constituent of turmeric ( Curcuma longa Linn.) and ginger ( Zingiber officinale Roscoe), respectively, against all four serotypes of DENV infecting human lung epithelial carcinoma (A549) cell line in vitro. Both compounds generated cell cytotoxicity to A549 cells at CC50 values of 108 µM for curcumin and 210 µM for 6‐gingerol. The compound curcumin showed antiviral properties as described by IC50 of 20.60, 13.95, 25.54, and 12.35 µM, while 6‐gingerol of 14.70, 14.17, 78.76, and 112.84 µM for DENV‐1, ‐2, ‐3, and ‐4, respectively. Different levels of antiviral properties were observed between DENV serotypes. Our findings suggest that the antiviral assay of compounds against DENV should be performed to all four serotypes and not limited to a particular serotype. In conclusion, curcumin and 6‐gingerol exhibit antiviral properties against DENV infection and could provide a new therapeutic approach for dengue disease treatment strategies.
登革热病毒(DENV)是在热带和亚热带地区引起登革热流行的最具地理广泛性的虫媒病毒。自然界提供了丰富的植物作为抗多种疾病的铅分子来源，包括DENV感染。我们分别研究了姜黄(Curcuma longa Linn.)和姜(Zingiber officinale Roscoe)的主要活性成分姜黄素和6 -姜辣素对感染人肺上皮癌(A549)细胞系的所有四种血清型DENV的体外抗病毒作用。这两种化合物在姜黄素108µM和6‐姜辣素210µM的CC50值下对A549细胞产生细胞毒性。化合物姜黄素对DENV‐1、‐2、‐3和‐4的IC50分别为20.60、13.95、25.54和12.35µM，而6‐姜辣素对DENV‐1、‐2、‐3和‐4的IC50分别为14.70、14.17、78.76和112.84µM。在DENV血清型之间观察到不同水平的抗病毒特性。我们的研究结果表明，化合物对DENV的抗病毒试验应针对所有四种血清型进行，而不限于特定的血清型。综上所述，姜黄素和6‐姜辣素对DENV感染具有抗病毒作用，可能为登革热的治疗策略提供新的治疗途径。
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