Pub Date : 2023-10-15DOI: 10.25303/1811rjbt2180222;
A. Rani, U. Siddiqui, T.K. Ghosh, N.N. Pandey
The individuals of diploid and triploid Schizothorax richardsonii (Gray, 1832) were identified using erythrocyte indices. The Erythrocyte cell's major axis of the triploid was 17% higher than the diploid. The increase in the nucleus major axis size of the erythrocyte of the triploid was also greater by 8% concerning the diploid fishes. The erythrocyte measurement ranged between 13.29±1.06 to 14.45±0.97 for diploid 15.91±1.32 to 16.49±1.23 for triploid erythrocyte nucleus 6.16±0.67 to 6.40±0.63 and 6.70±0.71 to 6.94±0.56 for diploid and triploid respectively. The data were analyzed by One Way of Analysis of Variance (ANOVA) for both diploid (control) and triploid (treated) erythrocyte and nucleus measurement which showed significant differences with p<0.05. These parameters, thus, can successfully be used in discriminating diploid and triploid S. richadrsonii.
利用红细胞指数对二倍体和三倍体理查森裂腹虫(Gray, 1832)进行了个体鉴定。三倍体的红细胞长轴比二倍体高17%。三倍体的红细胞细胞核长轴大小的增加也比二倍体大8%。红细胞计数二倍体为13.29±1.06 ~ 14.45±0.97，三倍体为15.91±1.32 ~ 16.49±1.23，二倍体为6.16±0.67 ~ 6.40±0.63，三倍体为6.70±0.71 ~ 6.94±0.56。二倍体(对照)和三倍体(处理)红细胞和细胞核测量数据采用单因素方差分析(One - Way of Variance Analysis, ANOVA)进行分析，两者差异显著(p < 0.05)。因此，这些参数可以成功地用于二倍体和三倍体的判别。
{"title":"Triploidy verification of Schizothorax richardsonii using erythrocyte cell and nucleus measurement","authors":"A. Rani, U. Siddiqui, T.K. Ghosh, N.N. Pandey","doi":"10.25303/1811rjbt2180222;","DOIUrl":"https://doi.org/10.25303/1811rjbt2180222;","url":null,"abstract":"The individuals of diploid and triploid Schizothorax richardsonii (Gray, 1832) were identified using erythrocyte indices. The Erythrocyte cell's major axis of the triploid was 17% higher than the diploid. The increase in the nucleus major axis size of the erythrocyte of the triploid was also greater by 8% concerning the diploid fishes. The erythrocyte measurement ranged between 13.29±1.06 to 14.45±0.97 for diploid 15.91±1.32 to 16.49±1.23 for triploid erythrocyte nucleus 6.16±0.67 to 6.40±0.63 and 6.70±0.71 to 6.94±0.56 for diploid and triploid respectively. The data were analyzed by One Way of Analysis of Variance (ANOVA) for both diploid (control) and triploid (treated) erythrocyte and nucleus measurement which showed significant differences with p<0.05. These parameters, thus, can successfully be used in discriminating diploid and triploid S. richadrsonii.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"108 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135766480","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 : 2023-10-15DOI: 10.25303/1811rjbt2640273
K.S. Dhondge, N.M. Maske, A.S. Khemnar
Identifying plants with desirable traits among existing plant varieties is the initial and most important step in plant breeding. Plant breeding requires the genetic variation of useful traits for crop improvement or crop betterment. The plant breeding depends upon the genetic variation. In nature, variation occurs mainly as a result of mutation and without it, plant breeding would be impossible. Mutation as a mechanism of creating variability was identified by Hugo de Vries while experimenting on the rediscovery of Mendel’s Law of Inheritance.17 Mutation arises in two ways; First, spontaneous mutation which occurs without treatment of the organism with an exogenous mutagen and secondly induced mutation which occurs due to the treatment of a plant or plant parts such as seed, stem, cuttings, pollen and ovules with the help of mutagens. The purposeful employment of the induced mutation for crop improvement is known as mutation breeding. The mutation breeding is also known as the variation breeding.There are mainly two types of mutagens (agent to cause mutation) i.e. physical and chemical mutagens. The mutant shows higher potential for improving plant architecture leading to better crop improvement and used as complementary and rational tool in plant breeding. Mutation breeding programme should be clearly planned and should be large enough with sufficient facilities to screen large population in short time. This review highlights the role of mutation breeding in improvement of qualitative and quantitative characters of crop plant.
{"title":"Mutation breeding as a tool for improving plant characters: A review","authors":"K.S. Dhondge, N.M. Maske, A.S. Khemnar","doi":"10.25303/1811rjbt2640273","DOIUrl":"https://doi.org/10.25303/1811rjbt2640273","url":null,"abstract":"Identifying plants with desirable traits among existing plant varieties is the initial and most important step in plant breeding. Plant breeding requires the genetic variation of useful traits for crop improvement or crop betterment. The plant breeding depends upon the genetic variation. In nature, variation occurs mainly as a result of mutation and without it, plant breeding would be impossible. Mutation as a mechanism of creating variability was identified by Hugo de Vries while experimenting on the rediscovery of Mendel’s Law of Inheritance.17 Mutation arises in two ways; First, spontaneous mutation which occurs without treatment of the organism with an exogenous mutagen and secondly induced mutation which occurs due to the treatment of a plant or plant parts such as seed, stem, cuttings, pollen and ovules with the help of mutagens. The purposeful employment of the induced mutation for crop improvement is known as mutation breeding. The mutation breeding is also known as the variation breeding.There are mainly two types of mutagens (agent to cause mutation) i.e. physical and chemical mutagens. The mutant shows higher potential for improving plant architecture leading to better crop improvement and used as complementary and rational tool in plant breeding. Mutation breeding programme should be clearly planned and should be large enough with sufficient facilities to screen large population in short time. This review highlights the role of mutation breeding in improvement of qualitative and quantitative characters of crop plant.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"114 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135761352","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 : 2023-10-15DOI: 10.25303/1811rjbt01150124
Kumar S.V. Praveen, John Indulekha, K. Valarmathy, B.K. Manjunatha
The present study investigated the application of central composite design in enhanced crude oil remediation using bacterial consortium. The bacterial strains viz. KG-2, SMG-8, NR-3 and OK-6(2) isolated from soil were selected for the crude oil utilization studies. The strains were identified as Pseudomonas stutzeri-KX344913, P. stutzeri-KX289657, Providencia rettgeri-KX289656 and P. rettgeri-KX344914 respectively using 16s rDNA sequence. The preliminary degradation was done using the DCPIP redox-indicator and further degradation was conducted by using Response Surface Methodology (RSM) and the analysis of variance and regression model. CCD model was developed and batch experiments were performed to understand the significance of the four variables (pH, temperature, salinity and inoculum concentration) on the TPH degradation process by applying CCD based RSM.
{"title":"Statistical Optimization of Crude Oil Degradation using Bacterial Consortium and their Enzymes","authors":"Kumar S.V. Praveen, John Indulekha, K. Valarmathy, B.K. Manjunatha","doi":"10.25303/1811rjbt01150124","DOIUrl":"https://doi.org/10.25303/1811rjbt01150124","url":null,"abstract":"The present study investigated the application of central composite design in enhanced crude oil remediation using bacterial consortium. The bacterial strains viz. KG-2, SMG-8, NR-3 and OK-6(2) isolated from soil were selected for the crude oil utilization studies. The strains were identified as Pseudomonas stutzeri-KX344913, P. stutzeri-KX289657, Providencia rettgeri-KX289656 and P. rettgeri-KX344914 respectively using 16s rDNA sequence. The preliminary degradation was done using the DCPIP redox-indicator and further degradation was conducted by using Response Surface Methodology (RSM) and the analysis of variance and regression model. CCD model was developed and batch experiments were performed to understand the significance of the four variables (pH, temperature, salinity and inoculum concentration) on the TPH degradation process by applying CCD based RSM.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"72 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135766319","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 : 2023-10-15DOI: 10.25303/1811rjbt2410252
S. Renganathan, A. Manjunath, A.G.V. Chinmayi, S. Sabat
This review highlights the growing emergence of antibiotic resistant bacterial strains. Antibiotics are slowly becoming redundant due to various mechanisms adopted by bacterial strains to combat the bactericidal properties of these antibiotics. Hence, the need of the hour is to find alternative methods of treatment of infections caused by these drug-resistant bacterial strains. The use of herbal products could be employed here as one of the possible solutions to curb the spread of bacterial infections. This review focuses solely on skin infections caused by bacteria. Numerous experiments have proven the bactericidal properties of Coriandrum sativum. Here, we explore the possibility of Coriandrum sativum as a solution to antimicrobial resistance.
{"title":"An Insight into understanding the Antimicrobial Activity of Coriandrum sativum on Antimicrobial Resistant Strains","authors":"S. Renganathan, A. Manjunath, A.G.V. Chinmayi, S. Sabat","doi":"10.25303/1811rjbt2410252","DOIUrl":"https://doi.org/10.25303/1811rjbt2410252","url":null,"abstract":"This review highlights the growing emergence of antibiotic resistant bacterial strains. Antibiotics are slowly becoming redundant due to various mechanisms adopted by bacterial strains to combat the bactericidal properties of these antibiotics. Hence, the need of the hour is to find alternative methods of treatment of infections caused by these drug-resistant bacterial strains. The use of herbal products could be employed here as one of the possible solutions to curb the spread of bacterial infections. This review focuses solely on skin infections caused by bacteria. Numerous experiments have proven the bactericidal properties of Coriandrum sativum. Here, we explore the possibility of Coriandrum sativum as a solution to antimicrobial resistance.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"21 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135766466","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}
Most cells of our body have primary cilia, which are specialised sensory organelles that are present on the apical surface. They have been proven to perform critical roles in tissue formation and signal transmission. Mutations of the genes involved in development and functioning of the cilia result in a group of diseases called as ciliopathies which are defined by organ failure caused by ciliary dysfunction. Numerous mutations result in renal ciliopathies that result in severe kidney diseases caused by ciliary dysfunction. The main emphasis of this review to set of overlapping and genetically heterogeneous disorders called ciliopathies with special emphasis on the renal involvement of these diseases. Renal involvement in these diseases ranges from a simple insignificant renal cyst to severe debilitating renal dysfunction resulting in renal failure in the early stage of the disease.
{"title":"Non-motile Ciliopathies of the Kidney","authors":"Barani Karikalan, Srikumar Chakravarthi, Prarthana Gopalakrishna Kalerammana","doi":"10.25303/1811rjbt2230232","DOIUrl":"https://doi.org/10.25303/1811rjbt2230232","url":null,"abstract":"Most cells of our body have primary cilia, which are specialised sensory organelles that are present on the apical surface. They have been proven to perform critical roles in tissue formation and signal transmission. Mutations of the genes involved in development and functioning of the cilia result in a group of diseases called as ciliopathies which are defined by organ failure caused by ciliary dysfunction. Numerous mutations result in renal ciliopathies that result in severe kidney diseases caused by ciliary dysfunction. The main emphasis of this review to set of overlapping and genetically heterogeneous disorders called ciliopathies with special emphasis on the renal involvement of these diseases. Renal involvement in these diseases ranges from a simple insignificant renal cyst to severe debilitating renal dysfunction resulting in renal failure in the early stage of the disease.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135766470","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 : 2023-10-15DOI: 10.25303/1811rjbt0960105
Manpreet Kaur, Divya Sharma, Reena Gupta
Out of fifty-three isolates isolated from soil samples of Tattapani hot spring of Himachal Pradesh, India, nineteen were screened for lipase production. Isolate TTP-06 with lipase activity of 3.01±0.05 U/ml was characterized and optimized for different production conditions to give maximum production of lipase. Isolate TTP-06 was identified as Bacillus subtilis TTP-06. Maximum enzyme activity was observed when 0.75% (v/v) of 24 hrs old inoculum was used in production medium (pH 8.0) containing 2.0% (v/v) olive oil, 0.75% (w/v) peptone, 0.75% (w/v) glucose, 0.3% (w/v) NaCl, 0.05% (w/v) MgSO4 and incubated at 55ºC under shaking conditions (150 rpm) for 24 hrs.
{"title":"Isolation of lipase producing thermotolerant Bacillus subtilis TTP-06 from hot spring of Himachal Pradesh","authors":"Manpreet Kaur, Divya Sharma, Reena Gupta","doi":"10.25303/1811rjbt0960105","DOIUrl":"https://doi.org/10.25303/1811rjbt0960105","url":null,"abstract":"Out of fifty-three isolates isolated from soil samples of Tattapani hot spring of Himachal Pradesh, India, nineteen were screened for lipase production. Isolate TTP-06 with lipase activity of 3.01±0.05 U/ml was characterized and optimized for different production conditions to give maximum production of lipase. Isolate TTP-06 was identified as Bacillus subtilis TTP-06. Maximum enzyme activity was observed when 0.75% (v/v) of 24 hrs old inoculum was used in production medium (pH 8.0) containing 2.0% (v/v) olive oil, 0.75% (w/v) peptone, 0.75% (w/v) glucose, 0.3% (w/v) NaCl, 0.05% (w/v) MgSO4 and incubated at 55ºC under shaking conditions (150 rpm) for 24 hrs.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135766473","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}
Secondary metabolites from bacterial sources are being seen as alternatives to identify new medicines for various disease conditions. Streptomyces is known to be a warehouse of secondary metabolites and is a promising source to be looked for the discovery and development of new anti-tumorigenic agents. Such identifications could alleviate the issue of lung cancer that takes over 2 million lives a year. In the current study, we have screened secondary metabolites from Streptomyces for their potential to act as drugs for non-small cell lung cancer. The metabolites were identified for their ability to inhibit RET protein. Gene fusion partners cause alteration to the RET protein that causes the cancer condition. The metabolites identified were based on docking, pharmacokinetics, toxicity and pass prediction. 16 metabolites from 13 different species of Streptomyces showed binding affinity to the target protein. Among the metabolites, melanin was the one that had strongest evident to act as a drug candidate for non-small cell lung cancer therapeutics.
{"title":"Screening Streptomyces secondary metabolites against non-small cell lung cancer using computational approaches","authors":"Sampath Kumar Vijayasarathy, Swaminathan Akila, Nithin Pranao Senthilkumar Rangasamy, Shanthi Veerappapillai","doi":"10.25303/1810rjbt0920106","DOIUrl":"https://doi.org/10.25303/1810rjbt0920106","url":null,"abstract":"Secondary metabolites from bacterial sources are being seen as alternatives to identify new medicines for various disease conditions. Streptomyces is known to be a warehouse of secondary metabolites and is a promising source to be looked for the discovery and development of new anti-tumorigenic agents. Such identifications could alleviate the issue of lung cancer that takes over 2 million lives a year. In the current study, we have screened secondary metabolites from Streptomyces for their potential to act as drugs for non-small cell lung cancer. The metabolites were identified for their ability to inhibit RET protein. Gene fusion partners cause alteration to the RET protein that causes the cancer condition. The metabolites identified were based on docking, pharmacokinetics, toxicity and pass prediction. 16 metabolites from 13 different species of Streptomyces showed binding affinity to the target protein. Among the metabolites, melanin was the one that had strongest evident to act as a drug candidate for non-small cell lung cancer therapeutics.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"41 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135486164","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}
Polyhydroxyalkanoate (PHA) is the naturally occurring biopolymer produced by the microorganisms. It is biodegradable and having physicochemical properties similar to conventional synthetic plastics and it can be used as an alternative to plastics. PHA is produced by microorganisms including bacteria, archaea and fungi. It gets accumulated inside the microorganisms as crystal in the presence of excess source of carbon, nitrogen, sulphur, oxygen and limited source of other nutrients. In this study PHA producing strain was isolated from agricultural soil sample. All the isolates obtained were screened for PHA production by using Nile red and Sudan black dyes. The potential isolate was characterized by biochemical tests and identified using 16S rRNA sequencing. The isolate showed sequence similarity with Priestia aryabhattai B8W22 and was designated as Priestia aryabhattai VITJK01. For PHA production, seed culture was prepared and inoculated in mineral salt medium containing glucose as a carbon source. PHA was extracted from cell dry weight biomass using methanolysis. It produced polyhydroxybutyrate (PHB) compounds including dodecane, penta decanoic acid, octadecanoic acid and heptadecanoic acid identified by Gas Chromatography Mass Spectrometry. Based on the results, it can be concluded that Priestia aryabhattai VITJK01 is a potential source for PHA/PHB production.
{"title":"Bioplastic (Polyhydroxyalkanoate) producing Indigenous Bacteria from Agricultural Soil Samples","authors":"Pratap Jyothirmayee Kola, Shravani Ratnakant Badme, Siddhi Avadhut Tendulkar, Sakshi Bhatt, Krishnan Kannabiran","doi":"10.25303/1810rjbt1390147","DOIUrl":"https://doi.org/10.25303/1810rjbt1390147","url":null,"abstract":"Polyhydroxyalkanoate (PHA) is the naturally occurring biopolymer produced by the microorganisms. It is biodegradable and having physicochemical properties similar to conventional synthetic plastics and it can be used as an alternative to plastics. PHA is produced by microorganisms including bacteria, archaea and fungi. It gets accumulated inside the microorganisms as crystal in the presence of excess source of carbon, nitrogen, sulphur, oxygen and limited source of other nutrients. In this study PHA producing strain was isolated from agricultural soil sample. All the isolates obtained were screened for PHA production by using Nile red and Sudan black dyes. The potential isolate was characterized by biochemical tests and identified using 16S rRNA sequencing. The isolate showed sequence similarity with Priestia aryabhattai B8W22 and was designated as Priestia aryabhattai VITJK01. For PHA production, seed culture was prepared and inoculated in mineral salt medium containing glucose as a carbon source. PHA was extracted from cell dry weight biomass using methanolysis. It produced polyhydroxybutyrate (PHB) compounds including dodecane, penta decanoic acid, octadecanoic acid and heptadecanoic acid identified by Gas Chromatography Mass Spectrometry. Based on the results, it can be concluded that Priestia aryabhattai VITJK01 is a potential source for PHA/PHB production.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135486299","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}
Renal cell carcinoma, sometimes referred to as kidney cancer, is a condition in which kidney cells develop into malignant (cancerous) tumours and expand rapidly. One of the 20 most prevalent malignancies in both male and female is kidney cancer (GLOBOCAN 2020). The risk of developing kidney cancer in the male population is about 1/46 (2.02%) and for women, it is about 1/80 (1.03%). Renal cancer is significantly easier to identify when the disease hallmarks are properly understood, boosting the likelihood of overall survival rates among patients. One of the key factors for promoting or inhibiting the renal cancer associated pathways is messenger RNA. Messenger RNAs are single stranded RNA coding protein formation and also influence their regulation. Differentially expressed RNAs are the genes which have a significant correlation with their coding protein. Hence, analysis of the differentially expressed RNAs linked with kidney cancer is required to understand their significance in the underlying biogenesis of cancer tumorigenesis. To identify all the differentially expressed RNAs, microarray analysis technique was used which is an efficient tool to carry out simultaneous evaluation of hundreds of genes' expression. By physically printing DNA sequence information encoding RNA for specific genes onto microarray "chips," it is feasible to detect the quantity of each RNA molecule in a biological sample. Using the data from microarray analysis in GEO2R, differentially expressed RNAs are retrieved and categorized according to their regulation. Enrichr is used to analyse these differentially expressed RNAs and identify their role in different signalling pathways, biological functions, cellular elements and molecular activities. The results from this comprehensive in silico platform shall aid in a novel understanding of the DEGs involved in cancer pathways which can further be utilized in an experimental setup. Hence, this study will help in better understanding of the role and expression of the differentially expressed RNAs in renal cell carcinoma.
{"title":"Identification and understanding association of differentially expressed RNA in Renal Cell Carcinoma","authors":"Niyanta Paul, Ritankar Tripathi, Sohini Chakraborty, Satarupa Banerjee","doi":"10.25303/1810rjbt035040","DOIUrl":"https://doi.org/10.25303/1810rjbt035040","url":null,"abstract":"Renal cell carcinoma, sometimes referred to as kidney cancer, is a condition in which kidney cells develop into malignant (cancerous) tumours and expand rapidly. One of the 20 most prevalent malignancies in both male and female is kidney cancer (GLOBOCAN 2020). The risk of developing kidney cancer in the male population is about 1/46 (2.02%) and for women, it is about 1/80 (1.03%). Renal cancer is significantly easier to identify when the disease hallmarks are properly understood, boosting the likelihood of overall survival rates among patients. One of the key factors for promoting or inhibiting the renal cancer associated pathways is messenger RNA. Messenger RNAs are single stranded RNA coding protein formation and also influence their regulation. Differentially expressed RNAs are the genes which have a significant correlation with their coding protein. Hence, analysis of the differentially expressed RNAs linked with kidney cancer is required to understand their significance in the underlying biogenesis of cancer tumorigenesis. To identify all the differentially expressed RNAs, microarray analysis technique was used which is an efficient tool to carry out simultaneous evaluation of hundreds of genes' expression. By physically printing DNA sequence information encoding RNA for specific genes onto microarray \"chips,\" it is feasible to detect the quantity of each RNA molecule in a biological sample. Using the data from microarray analysis in GEO2R, differentially expressed RNAs are retrieved and categorized according to their regulation. Enrichr is used to analyse these differentially expressed RNAs and identify their role in different signalling pathways, biological functions, cellular elements and molecular activities. The results from this comprehensive in silico platform shall aid in a novel understanding of the DEGs involved in cancer pathways which can further be utilized in an experimental setup. Hence, this study will help in better understanding of the role and expression of the differentially expressed RNAs in renal cell carcinoma.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135486566","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}
The rapid activation of signaling pathways is the primary factor responsible for the progression of serious malignancies. Particularly, overexpression of β-catenin is one of the preventative oncogenic biomarkers that is widely present in many tumor types. Therefore, we have designed an integrated pharmacophore strategy to discover the potential inhibitor against β-catenin. Primarily, the ligand-, energy-optimized and the receptor cavity-based pharmacophore hypothesis AAHHR, ADR and ANNNRRR were constructed to screen the active molecules from the database. In order to improve the screening efficacy, the resultant molecules were scrutinized by integrating the results obtained through docking and MM/GBSA calculations. Further, the common hit molecules were subjected to a pharmacokinetic and toxicity study which resulted in two potent β-catenin inhibitors: BAS03014832 and BAS01077671. The existence of thiazole and pyrazole moiety is responsible for the anti-neoplastic activity of these molecules. Finally, a deep neural network technique was used to assess the inhibitory action of these compounds across 66 colorectal cancer cell lines. Overall, the results of our study portray a pathway for the experimental biologist in developing selective β-catenin inhibitors.
{"title":"Discovery of small molecule modulators targeting β-catenin interactions using molecular docking and molecular dynamics strategy","authors":"Shanthi Veerappapillai, Aman Hussain","doi":"10.25303/1810rjbt024034","DOIUrl":"https://doi.org/10.25303/1810rjbt024034","url":null,"abstract":"The rapid activation of signaling pathways is the primary factor responsible for the progression of serious malignancies. Particularly, overexpression of β-catenin is one of the preventative oncogenic biomarkers that is widely present in many tumor types. Therefore, we have designed an integrated pharmacophore strategy to discover the potential inhibitor against β-catenin. Primarily, the ligand-, energy-optimized and the receptor cavity-based pharmacophore hypothesis AAHHR, ADR and ANNNRRR were constructed to screen the active molecules from the database. In order to improve the screening efficacy, the resultant molecules were scrutinized by integrating the results obtained through docking and MM/GBSA calculations. Further, the common hit molecules were subjected to a pharmacokinetic and toxicity study which resulted in two potent β-catenin inhibitors: BAS03014832 and BAS01077671. The existence of thiazole and pyrazole moiety is responsible for the anti-neoplastic activity of these molecules. Finally, a deep neural network technique was used to assess the inhibitory action of these compounds across 66 colorectal cancer cell lines. Overall, the results of our study portray a pathway for the experimental biologist in developing selective β-catenin inhibitors.","PeriodicalId":21091,"journal":{"name":"Research Journal of Biotechnology","volume":"58 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-09-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135486563","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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