Pub Date : 2021-06-01DOI: 10.30491/JABR.2021.130934
Ali Abasiyan, Ebrhim Motevalian, A. Latifi, Soraya Emamgholizadeh Minaei
Introduction: Although radiation is recognized as the most effective nonsurgical treatment, the outcomes and control rates are generally poor. However, a combination of radiation therapy with hyperthermia and chemotherapy can improve the efficacy of treatment. The aim was to explore the potential of morphological and gradient-based features on microscopic images in improving the identification accuracy of subtle differences in cell structure during different treatments. Materials and Methods: Fifty single-cell images were used for each group and treatment regimen. The groups were individually subjected to: 1) hyperthermia at 43°C; 2) temozolomide (TMZ) chemotherapy at 10% inhibitory concentration; 3) radiotherapy at 2Gy; 4) combination of TMZ chemotherapy and hyperthermia; 5) combination of radiotherapy and hyperthermia; 6) combination of TMZ chemotherapy and radiotherapy; and 7) combination of TMZ chemotherapy, radiotherapy, and hyperthermia. Morphological and gradient-based features were extracted from each cell. The area under the receiver operating characteristic curve (AUC) was calculated for each significant feature to evaluate the performance of cell change detection. Results: According to AUCs, gradient-based features showed superior performance to morphological features in identifying cell changes during all treatment regimens in all groups. In this regard, the AUC of the gradient-mean feature exceeded 0.599 for all groups. The ratio of maximum to minimum cell diameter was the best morphological feature, with an AUC above 0.588 for all groups. Conclusions: Quantitative analysis of features is a reliable indicator of damage, with the potential to characterize cell changes during treatment regimens.
{"title":"A Quantitative Multivariate Microscopic Analysis for Identifying Changes of Glioblastoma Cancer Cells due to Thermochemoradiation Therapy","authors":"Ali Abasiyan, Ebrhim Motevalian, A. Latifi, Soraya Emamgholizadeh Minaei","doi":"10.30491/JABR.2021.130934","DOIUrl":"https://doi.org/10.30491/JABR.2021.130934","url":null,"abstract":"Introduction: Although radiation is recognized as the most effective nonsurgical treatment, the outcomes and control rates are generally poor. However, a combination of radiation therapy with hyperthermia and chemotherapy can improve the efficacy of treatment. The aim was to explore the potential of morphological and gradient-based features on microscopic images in improving the identification accuracy of subtle differences in cell structure during different treatments. Materials and Methods: Fifty single-cell images were used for each group and treatment regimen. The groups were individually subjected to: 1) hyperthermia at 43°C; 2) temozolomide (TMZ) chemotherapy at 10% inhibitory concentration; 3) radiotherapy at 2Gy; 4) combination of TMZ chemotherapy and hyperthermia; 5) combination of radiotherapy and hyperthermia; 6) combination of TMZ chemotherapy and radiotherapy; and 7) combination of TMZ chemotherapy, radiotherapy, and hyperthermia. Morphological and gradient-based features were extracted from each cell. The area under the receiver operating characteristic curve (AUC) was calculated for each significant feature to evaluate the performance of cell change detection. Results: According to AUCs, gradient-based features showed superior performance to morphological features in identifying cell changes during all treatment regimens in all groups. In this regard, the AUC of the gradient-mean feature exceeded 0.599 for all groups. The ratio of maximum to minimum cell diameter was the best morphological feature, with an AUC above 0.588 for all groups. Conclusions: Quantitative analysis of features is a reliable indicator of damage, with the potential to characterize cell changes during treatment regimens.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"8 1","pages":"155-163"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42754148","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 : 2021-06-01DOI: 10.30491/JABR.2020.237662.1248
Arockiyajainmary Michealsamy, Lokesh Thangamani, G. Manivel, Praveen Kumar, Shobana Sundar, Shanmughavel Piramanayagam, J. Natarajan
Microorganisms are ubiquitous in nature. They are found across diverse biosphere and greatly vary among them. Several beneficial microbes engaging in degradation and their services to the ecosystem have not been fully explored. This tangled module could be resolved by Meta 'omics' approach and analysing their molecular interaction with the environment. In our day-to-day life, human beings are exposed to various xenobiotics in the form of drugs/pharmaceuticals, pesticides, artificially flavoured food and beverages. Newer diseases are also emerging due to environmental pollutants. Bioremediation offers an effective way to resilient our fragile planet. Next-generation sequencing became an ultimate technique to unravel the significance of the microbiome in remediating polluted lands and sludges. Integrating the meta omics data would open new perspectives in the clean-up of toxic contaminants from our environment. Through this review, we attempted to explore the potential of meta-omics approaches in deciphering the eavesdropping of complex microbes. This review provides novel insights into the Meta-omics techniques that aid in the field of bioremediation.
{"title":"Current Research and Applications of Meta-omics Stratagems in Bioremediation: A Bird’s-Eye View","authors":"Arockiyajainmary Michealsamy, Lokesh Thangamani, G. Manivel, Praveen Kumar, Shobana Sundar, Shanmughavel Piramanayagam, J. Natarajan","doi":"10.30491/JABR.2020.237662.1248","DOIUrl":"https://doi.org/10.30491/JABR.2020.237662.1248","url":null,"abstract":"Microorganisms are ubiquitous in nature. They are found across diverse biosphere and greatly vary among them. Several beneficial microbes engaging in degradation and their services to the ecosystem have not been fully explored. This tangled module could be resolved by Meta 'omics' approach and analysing their molecular interaction with the environment. In our day-to-day life, human beings are exposed to various xenobiotics in the form of drugs/pharmaceuticals, pesticides, artificially flavoured food and beverages. Newer diseases are also emerging due to environmental pollutants. Bioremediation offers an effective way to resilient our fragile planet. Next-generation sequencing became an ultimate technique to unravel the significance of the microbiome in remediating polluted lands and sludges. Integrating the meta omics data would open new perspectives in the clean-up of toxic contaminants from our environment. Through this review, we attempted to explore the potential of meta-omics approaches in deciphering the eavesdropping of complex microbes. This review provides novel insights into the Meta-omics techniques that aid in the field of bioremediation.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"8 1","pages":"109-115"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49596822","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 : 2021-06-01DOI: 10.30491/JABR.2021.243285.1271
F. Izadi, Mohammad Hasan Soheilifar, Hoda Keshmiri Neghab, Mahya Soheilifar, R. Amini
Introduction: Understanding the association among various disorders has remarkably improved their diagnosis and therapies. It has been observed that autism and inflammatory bowel diseases cause a sort of inflammation. Exploring the relationship between them will lead to discovering important involved genes and in turn will eventually help discover any possible common therapeutic protocols. The aim of the present study was to determine the correlation between autism spectrum disorders and inflammatory bowel diseases. Materials and Methods: The common genes associated with autism spectrum disorders and inflammatory bowel diseases were retrieved from DisGeNET. SFARI databases and were subjected to an in silico data analysis framework to explore predictive genes and the related pathways. Results: Eleven genes including HLA-DRB1, MTHFR, PON1, IL6, MTOR, SETD2, GSTM1, APC, IFNG, SERPINE1, and MAPK1 regulated by YY1 and IRF1 transcription factors were characterized as discriminating molecules which by further screening were enriched in pathways mostly involved in neutrophil apoptosis, neutrophil homeostasis, chemokine biosynthesis and the regulation of immune system response. Conclusions: According to findings it can be stated that the identified common genes were associated with a wide range of pathogenic mechanisms.
{"title":"Exploring Transcriptional Relationships Implicated in Autism and Inflammatory Bowel Diseases Using Systems Biology Approaches","authors":"F. Izadi, Mohammad Hasan Soheilifar, Hoda Keshmiri Neghab, Mahya Soheilifar, R. Amini","doi":"10.30491/JABR.2021.243285.1271","DOIUrl":"https://doi.org/10.30491/JABR.2021.243285.1271","url":null,"abstract":"Introduction: Understanding the association among various disorders has remarkably improved their diagnosis and therapies. It has been observed that autism and inflammatory bowel diseases cause a sort of inflammation. Exploring the relationship between them will lead to discovering important involved genes and in turn will eventually help discover any possible common therapeutic protocols. The aim of the present study was to determine the correlation between autism spectrum disorders and inflammatory bowel diseases. Materials and Methods: The common genes associated with autism spectrum disorders and inflammatory bowel diseases were retrieved from DisGeNET. SFARI databases and were subjected to an in silico data analysis framework to explore predictive genes and the related pathways. Results: Eleven genes including HLA-DRB1, MTHFR, PON1, IL6, MTOR, SETD2, GSTM1, APC, IFNG, SERPINE1, and MAPK1 regulated by YY1 and IRF1 transcription factors were characterized as discriminating molecules which by further screening were enriched in pathways mostly involved in neutrophil apoptosis, neutrophil homeostasis, chemokine biosynthesis and the regulation of immune system response. Conclusions: According to findings it can be stated that the identified common genes were associated with a wide range of pathogenic mechanisms.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"8 1","pages":"180-185"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42256354","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 : 2021-06-01DOI: 10.30491/JABR.2021.255549.1308
Danilo C. Sabarre, Camila Flor Yagonia-Lobarbio
Polyphenol oxidase (PPO) is a copper-containing enzyme that can be used for different applications including wastewater treatment and biosensing. Given these wide arrays of application, the reaction and biochemical characteristics of the enzyme must be known to further determine its other applications and to control the essential factors during processing. The purpose of this research was to review the different factors that influence the effective extraction and characterization of PPO from plant materials. The pH of the extraction mixture, extraction temperature, type of buffer, mass to solvent ratio, extraction time, and additives are the factors that influence the effective extraction of PPO from plant materials. Since PPOs taken from different plant sources have varied protein structures, these factors have different effects during extraction. The isolated PPO from the extraction process can be characterized based on its activity as a function of pH, temperature, and type of substrate, and on the values of its kinetic parameters (Km and Vmax). PPO isolated from different plant sources shows varied optimum pH, optimum temperature, substrate affinity, and kinetic parameter values.
{"title":"Extraction and Characterization of Polyphenol Oxidase from Plant Materials: A Review","authors":"Danilo C. Sabarre, Camila Flor Yagonia-Lobarbio","doi":"10.30491/JABR.2021.255549.1308","DOIUrl":"https://doi.org/10.30491/JABR.2021.255549.1308","url":null,"abstract":"Polyphenol oxidase (PPO) is a copper-containing enzyme that can be used for different applications including wastewater treatment and biosensing. Given these wide arrays of application, the reaction and biochemical characteristics of the enzyme must be known to further determine its other applications and to control the essential factors during processing. The purpose of this research was to review the different factors that influence the effective extraction and characterization of PPO from plant materials. The pH of the extraction mixture, extraction temperature, type of buffer, mass to solvent ratio, extraction time, and additives are the factors that influence the effective extraction of PPO from plant materials. Since PPOs taken from different plant sources have varied protein structures, these factors have different effects during extraction. The isolated PPO from the extraction process can be characterized based on its activity as a function of pH, temperature, and type of substrate, and on the values of its kinetic parameters (Km and Vmax). PPO isolated from different plant sources shows varied optimum pH, optimum temperature, substrate affinity, and kinetic parameter values.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"8 1","pages":"83-95"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42890814","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 : 2021-06-01DOI: 10.30491/JABR.2020.233148.1232
Sulav Indra Paul, B. Majumdar, Rakib Ehsan, M. Hasan, Arpan Baidya, Mohammad Akibul Hasan Bakky
The ocean is considered to be an immense reservoir of biological and microbial diversity on the planet. In marine biospheres, microbial communities are ecologically significant as intermediaries of energy. By decomposing the dead as well as decaying organic matter with the assistance of microbial communities, it plays an indispensable role in the nutrient regeneration cycles of marine ecosystems. Marine environments associated with microorganisms such as bacteria, fungi, and bacterial virus have renowned potential to produce novel bioactive natural products and chemically diverse secondary metabolites like antibiotics, antifungal, antiviral, antitumor, anticancer, and also different hydrolyzing enzymes, namely, protease, lipase, amylase, chitinase, etc. Hence, the bioprospecting for these compounds is of greater importance. Numerous effective and efficient applications of marine microbial metabolites contribute to the fields of pharmaceuticals, biotechnological, agricultural, cosmetics industries, and so on. This review attempts to summarize the present status of bioprospecting marine microorganisms and their role in natural product discovery.
{"title":"Bioprospecting Potential of Marine Microbial Natural Bioactive Compounds","authors":"Sulav Indra Paul, B. Majumdar, Rakib Ehsan, M. Hasan, Arpan Baidya, Mohammad Akibul Hasan Bakky","doi":"10.30491/JABR.2020.233148.1232","DOIUrl":"https://doi.org/10.30491/JABR.2020.233148.1232","url":null,"abstract":"The ocean is considered to be an immense reservoir of biological and microbial diversity on the planet. In marine biospheres, microbial communities are ecologically significant as intermediaries of energy. By decomposing the dead as well as decaying organic matter with the assistance of microbial communities, it plays an indispensable role in the nutrient regeneration cycles of marine ecosystems. Marine environments associated with microorganisms such as bacteria, fungi, and bacterial virus have renowned potential to produce novel bioactive natural products and chemically diverse secondary metabolites like antibiotics, antifungal, antiviral, antitumor, anticancer, and also different hydrolyzing enzymes, namely, protease, lipase, amylase, chitinase, etc. Hence, the bioprospecting for these compounds is of greater importance. Numerous effective and efficient applications of marine microbial metabolites contribute to the fields of pharmaceuticals, biotechnological, agricultural, cosmetics industries, and so on. This review attempts to summarize the present status of bioprospecting marine microorganisms and their role in natural product discovery.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"8 1","pages":"96-108"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"45007791","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 : 2021-06-01DOI: 10.30491/JABR.2021.130940
Foozieh Moghadami, R. Hosseini, J. Fooladi, M. Kalantari
Introduction: Coenzyme Q10 is one of the antioxidants with a worldwide market. Nowadays the coenzymeQ10 production has been considered by fermentation using microorganisms. In this study, the Response Surface Methodology was used to optimize culture composition for coenzyme Q10 production by a previously isolated bacterium, Gluconobacter japonicus FM10. Materials and methods: A central composite design was employed to optimize the culture composition including sorbitol, yeast extract, peptone, KH2PO4, and MgSO4 for coenzyme Q10 production. The dry cell weight and coenzymeQ10 concentration were monitored as response variables and the desirability function approach was applied to obtain the optimum level for each factor. Results: Results showed that an average, 3 mg/L of coenzyme Q10 was obtained when the optimized culture composition was employed (110 g/L of sorbitol, 25 g/L of yeast extract, 35 g/L of peptone, 0.5 g/L of KH2PO4, and 0.55 g/L of MgSO4). In addition, the expected dry cell weight reached 6 g/L in the presence of 90 g/L of sorbitol, 17.5 g/L of yeast extract, 35 g/L of peptone, 0 g/L of KH2PO4, and 1.7 g/L of MgSO4. Conclusions: The results of regression analysis revealed that the concentrations of peptone and sorbitol were the most effective factors in producing coenzyme Q10 and dry cell weight, respectively.
{"title":"Optimization of Coenzyme Q10 Production by Gluconobacter japonicus FM10 Using Response Surface Methodology","authors":"Foozieh Moghadami, R. Hosseini, J. Fooladi, M. Kalantari","doi":"10.30491/JABR.2021.130940","DOIUrl":"https://doi.org/10.30491/JABR.2021.130940","url":null,"abstract":"Introduction: Coenzyme Q10 is one of the antioxidants with a worldwide market. Nowadays the coenzymeQ10 production has been considered by fermentation using microorganisms. In this study, the Response Surface Methodology was used to optimize culture composition for coenzyme Q10 production by a previously isolated bacterium, Gluconobacter japonicus FM10. Materials and methods: A central composite design was employed to optimize the culture composition including sorbitol, yeast extract, peptone, KH2PO4, and MgSO4 for coenzyme Q10 production. The dry cell weight and coenzymeQ10 concentration were monitored as response variables and the desirability function approach was applied to obtain the optimum level for each factor. Results: Results showed that an average, 3 mg/L of coenzyme Q10 was obtained when the optimized culture composition was employed (110 g/L of sorbitol, 25 g/L of yeast extract, 35 g/L of peptone, 0.5 g/L of KH2PO4, and 0.55 g/L of MgSO4). In addition, the expected dry cell weight reached 6 g/L in the presence of 90 g/L of sorbitol, 17.5 g/L of yeast extract, 35 g/L of peptone, 0 g/L of KH2PO4, and 1.7 g/L of MgSO4. Conclusions: The results of regression analysis revealed that the concentrations of peptone and sorbitol were the most effective factors in producing coenzyme Q10 and dry cell weight, respectively.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"8 1","pages":"172-179"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42294484","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 : 2021-06-01DOI: 10.30491/JABR.2020.238953.1253
A. Surti, S. Mhatre
Introduction: Inulinases are β-fructohydrolase enzymes that catalyze the hydrolysis of inulin. Recently, this enzyme has gained much importance mainly due to its ability to produce high-density fructose syrup using inulin as a raw material. In the current study, screening of inulinase-producing microorganisms was carried out from the rhizosphere soil of the Dahlia plant and rotten garlic samples. Materials and Methods: The inulinase activity was detected with the help of 3,5-dinitrosalicylic acid (DNSA) and Seliwanoff’s method, and the organism showing the highest potential was selected for further optimization studies. Results: The optimum culture conditions for inulinase production, by the test fungal culture, were observed when 5% inoculum was added to the minimal medium (pH 5.5) containing 1% inulin/ costus root powder as a carbon source and 0.15% NaNO3/ NH4Cl as a nitrogen source, and incubated at 30°C for 48h under shaker conditions (200 rpm). Maximum enzyme activity was observed at pH level of 5 and temperature level of 45°C, with thermal stability noted between 35°C-55°C. The I/S value of the crude enzyme was calculated to be 0.45 indicating true inulinase activity. It showed no significant inhibition in the presence of metal ions such as Zn+2, Mg+2, and Fe+3. The Ca+2 ions showed partial inhibition whereas Cu+2 ions showed an enhancement in the enzyme activity. Conclusions: These factors may present the test fungal culture isolated in the present study to be a potential candidate for the production of thermo-tolerant and metal resistant inulinase enzyme in order to be used for various biotechnological processes.
{"title":"Optimization of Inulinase Production by a Fungal Species Isolated From Rotten Garlic Samples","authors":"A. Surti, S. Mhatre","doi":"10.30491/JABR.2020.238953.1253","DOIUrl":"https://doi.org/10.30491/JABR.2020.238953.1253","url":null,"abstract":"Introduction: Inulinases are β-fructohydrolase enzymes that catalyze the hydrolysis of inulin. Recently, this enzyme has gained much importance mainly due to its ability to produce high-density fructose syrup using inulin as a raw material. In the current study, screening of inulinase-producing microorganisms was carried out from the rhizosphere soil of the Dahlia plant and rotten garlic samples. Materials and Methods: The inulinase activity was detected with the help of 3,5-dinitrosalicylic acid (DNSA) and Seliwanoff’s method, and the organism showing the highest potential was selected for further optimization studies. Results: The optimum culture conditions for inulinase production, by the test fungal culture, were observed when 5% inoculum was added to the minimal medium (pH 5.5) containing 1% inulin/ costus root powder as a carbon source and 0.15% NaNO3/ NH4Cl as a nitrogen source, and incubated at 30°C for 48h under shaker conditions (200 rpm). Maximum enzyme activity was observed at pH level of 5 and temperature level of 45°C, with thermal stability noted between 35°C-55°C. The I/S value of the crude enzyme was calculated to be 0.45 indicating true inulinase activity. It showed no significant inhibition in the presence of metal ions such as Zn+2, Mg+2, and Fe+3. The Ca+2 ions showed partial inhibition whereas Cu+2 ions showed an enhancement in the enzyme activity. Conclusions: These factors may present the test fungal culture isolated in the present study to be a potential candidate for the production of thermo-tolerant and metal resistant inulinase enzyme in order to be used for various biotechnological processes.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"8 1","pages":"164-171"},"PeriodicalIF":0.0,"publicationDate":"2021-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"42869452","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 : 2021-04-25DOI: 10.30491/JABR.2021.255853.1310
Leila Mousavizadeh, S. Ghasemi
One of the main reasons for the high prevalence of SARS-CoV2 is the high speed of its replication and reproduction. The replication inhibitors are under investigation due to the importance of prevention of the spread of coronavirus disease 2019 (COVID-19). In coronavirus replication, the virus enters the cell by endocytosis. After uncoating, the positive-strand RNA is translated to produce the non-structural protein (NCP) precursors. These precursors are cleaved and form mature, functional helicase and RNA polymerase. A replication-transcription complex (RTC) is then formed. Targeting the various stages of this process may be useful in preventing the spread of this epidemic. According to the similarity of COVID-19 replication to the other single-stranded RNA viruses such as HCV, Ebola Virus, and Marburg, the best way to prevent the spread of infection is the viral genome replication targeting with specific drugs after exposure to the virus. For COVID-19 medications, and compounds that target SARS-CoV2 replication are being tested in silico, in vitro, or in vivo, and according to other clinical trials that have been applied for SARS-CoV and MERS-CoV. Inhibitor drugs in the attachment, protease, and replication stages can prevent the virus from multiplying. By reviewing previous related articles in this field, in this review article, we are trying to focus on all information related to genome replication and categorize known drugs that have been applied as clinical trial treatments. The use of these drugs and other medications seems to be effective in reducing the prevalence of COVID-19.
{"title":"Suppressing SARS-CoV2 Genome Replication: A Way to Overcome the Rate of Spread","authors":"Leila Mousavizadeh, S. Ghasemi","doi":"10.30491/JABR.2021.255853.1310","DOIUrl":"https://doi.org/10.30491/JABR.2021.255853.1310","url":null,"abstract":"One of the main reasons for the high prevalence of SARS-CoV2 is the high speed of its replication and reproduction. The replication inhibitors are under investigation due to the importance of prevention of the spread of coronavirus disease 2019 (COVID-19). In coronavirus replication, the virus enters the cell by endocytosis. After uncoating, the positive-strand RNA is translated to produce the non-structural protein (NCP) precursors. These precursors are cleaved and form mature, functional helicase and RNA polymerase. A replication-transcription complex (RTC) is then formed. Targeting the various stages of this process may be useful in preventing the spread of this epidemic. According to the similarity of COVID-19 replication to the other single-stranded RNA viruses such as HCV, Ebola Virus, and Marburg, the best way to prevent the spread of infection is the viral genome replication targeting with specific drugs after exposure to the virus. For COVID-19 medications, and compounds that target SARS-CoV2 replication are being tested in silico, in vitro, or in vivo, and according to other clinical trials that have been applied for SARS-CoV and MERS-CoV. Inhibitor drugs in the attachment, protease, and replication stages can prevent the virus from multiplying. By reviewing previous related articles in this field, in this review article, we are trying to focus on all information related to genome replication and categorize known drugs that have been applied as clinical trial treatments. The use of these drugs and other medications seems to be effective in reducing the prevalence of COVID-19.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47261359","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 : 2021-03-09DOI: 10.30491/JABR.2020.223247.1197
S. Karimi, A. Alizadeh, Nasibe Tabibi, S. Ghasemi
The clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) used for genome editing. The usage of CRISPR-Cas9 in gene editing is faced with certain limitations including off-target mutation, decreased homologous recombination (HR) repair, and immune system responses. It seems that if Cas9 expressed in an inducible manner, off-target mutations may decrease. P53 decreases the activity of the HR pathway in the cell cycle, so, the decrease in P53 level may increase the activity of this pathway. Based on this topic, for the first time, we designed ''px601-Turbo GFP-TRE-shRNA P53'' as a CRISPR-based vector. The use of this vector can simultaneously induce expression of Cas9 and shutdown transiently P53 under an inducible promoter and an inducing agent. Therefore, shutdown transiently P53 may be leading to reduced off-targets and increased accuracy of genome editing. In the human gastric cancer MKN45 cell line, the P53 gene expresses at a normal level. Also, CD44 in this cell line has overexpression and is a gastric cancer stem cell marker. To evaluate this hypothesis, CD44 will be targeted for a specific sequence change (editing) by the px601-Turbo GFP-TRE-shRNA P53 vector. Accordingly, after cloning and virus preparation, MKN45 cell lines will be transduced in the presence of the appropriate doxycycline (DOX) dosage. Ultimately, to evaluate the vector efficiency, DNA extraction and whole-genome sequencing (WGS) will be done and compared with the transduced MKN45 cells without an inducible prompter and DOX as control. Also, the Sanger sequencing for the target gene must be done. This temporary inducible expression may appear to increase the efficiency of the CD44 gene editing and reduce off-targets.
{"title":"Increase the Efficiency of MKN45 Cell Line to CD44 Editing by CRISPR/Cas9: A Hypothesis About P53 Suppression in Gene Editing","authors":"S. Karimi, A. Alizadeh, Nasibe Tabibi, S. Ghasemi","doi":"10.30491/JABR.2020.223247.1197","DOIUrl":"https://doi.org/10.30491/JABR.2020.223247.1197","url":null,"abstract":"The clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) used for genome editing. The usage of CRISPR-Cas9 in gene editing is faced with certain limitations including off-target mutation, decreased homologous recombination (HR) repair, and immune system responses. It seems that if Cas9 expressed in an inducible manner, off-target mutations may decrease. P53 decreases the activity of the HR pathway in the cell cycle, so, the decrease in P53 level may increase the activity of this pathway. Based on this topic, for the first time, we designed ''px601-Turbo GFP-TRE-shRNA P53'' as a CRISPR-based vector. The use of this vector can simultaneously induce expression of Cas9 and shutdown transiently P53 under an inducible promoter and an inducing agent. Therefore, shutdown transiently P53 may be leading to reduced off-targets and increased accuracy of genome editing. In the human gastric cancer MKN45 cell line, the P53 gene expresses at a normal level. Also, CD44 in this cell line has overexpression and is a gastric cancer stem cell marker. To evaluate this hypothesis, CD44 will be targeted for a specific sequence change (editing) by the px601-Turbo GFP-TRE-shRNA P53 vector. Accordingly, after cloning and virus preparation, MKN45 cell lines will be transduced in the presence of the appropriate doxycycline (DOX) dosage. Ultimately, to evaluate the vector efficiency, DNA extraction and whole-genome sequencing (WGS) will be done and compared with the transduced MKN45 cells without an inducible prompter and DOX as control. Also, the Sanger sequencing for the target gene must be done. This temporary inducible expression may appear to increase the efficiency of the CD44 gene editing and reduce off-targets.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"41779803","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 : 2021-03-01DOI: 10.30491/JABR.2020.231423.1228
S. Jahanfar, M. Ghavami, K. Khosravi‐Darani, M. Jahadi
Introduction: Although Green tea is a rich source of antioxidant, use of this herbal in food industries is limited due to its oxygen and light instabilities. Materials and Methods: Green tea polyphenols were encapsulated into liposomes using Mozafari method (with no solvents and detergents) to improve bioavailability of tea polyphenols. Screening design was used to find the major variables within all possible process variables. Then, optimal conditions were studied using response surface. Results: The most appropriate condition was achieved using phosphatidylcholine of 4.5% (w/w), extract concentration of 0.7%, mixing time of 30 min and temperature of 50 °C. Encapsulation efficiency (EE) depended on concentrations of the green tea extract and phosphatidylcholine. The EE in optimal formulation was reached as 51.34%. The particle size and Z-potential of liposomal green tea extract were assessed at 419 nm and -59.7 mV, respectively. The total polyphenol content (TPC) of green tea included 164.2 mg gallic acid/g extract. Free radical scavenging activities of free and liposomal extracts were calculated as 90.6 and 93.37%, respectively, using 2-2-diphenyl-1-pycrylhydrazyl (DPPH) method. Conclusions: Results revealed that liposomal green tea extract can be used extensively in food industries due to its high antioxidant activity. No size decreasing methods (e.g. sonication and homogenization) were needed to produce nanosize liposomal extracts to avoid structure instability.
{"title":"Liposomal Green Tea Extract: Optimization and Physicochemical Characterization","authors":"S. Jahanfar, M. Ghavami, K. Khosravi‐Darani, M. Jahadi","doi":"10.30491/JABR.2020.231423.1228","DOIUrl":"https://doi.org/10.30491/JABR.2020.231423.1228","url":null,"abstract":"Introduction: Although Green tea is a rich source of antioxidant, use of this herbal in food industries is limited due to its oxygen and light instabilities. Materials and Methods: Green tea polyphenols were encapsulated into liposomes using Mozafari method (with no solvents and detergents) to improve bioavailability of tea polyphenols. Screening design was used to find the major variables within all possible process variables. Then, optimal conditions were studied using response surface. Results: The most appropriate condition was achieved using phosphatidylcholine of 4.5% (w/w), extract concentration of 0.7%, mixing time of 30 min and temperature of 50 °C. Encapsulation efficiency (EE) depended on concentrations of the green tea extract and phosphatidylcholine. The EE in optimal formulation was reached as 51.34%. The particle size and Z-potential of liposomal green tea extract were assessed at 419 nm and -59.7 mV, respectively. The total polyphenol content (TPC) of green tea included 164.2 mg gallic acid/g extract. Free radical scavenging activities of free and liposomal extracts were calculated as 90.6 and 93.37%, respectively, using 2-2-diphenyl-1-pycrylhydrazyl (DPPH) method. Conclusions: Results revealed that liposomal green tea extract can be used extensively in food industries due to its high antioxidant activity. No size decreasing methods (e.g. sonication and homogenization) were needed to produce nanosize liposomal extracts to avoid structure instability.","PeriodicalId":14945,"journal":{"name":"Journal of Applied Biotechnology Reports","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"49257576","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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