Pub Date : 2022-01-01DOI: 10.33545/26646536.2022.v4.i1a.37
R. K. Nayak, A. Hussain, K. Prajapat, M. Gurjar
{"title":"Influence of abiotic and biotic factors on seasonal abundance of brinjal shoot and fruit borer, Leucinodes orbonalis Guenee","authors":"R. K. Nayak, A. Hussain, K. Prajapat, M. Gurjar","doi":"10.33545/26646536.2022.v4.i1a.37","DOIUrl":"https://doi.org/10.33545/26646536.2022.v4.i1a.37","url":null,"abstract":"","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88347669","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 : 2022-01-01DOI: 10.17706/ijbbb.2022.12.2.39-42
Ruolin Liu
: Covid - 19 virus has infected tens of millions of people since 2020. Its extremely high mortality rate has a huge impact on the development of the world. The influence of new coronavirus on the human body was discussed from two aspects: Antibody level and virus - cell attack. In addition, the study of the impact of the virus on the human body, expands the content of vaccine development and introduction. We can accurately study the relationship between the two through their structural differences, so as to have a good grasp of the structure of the vaccine.
{"title":"The Influence of Novel Coronavirus on Human Body System","authors":"Ruolin Liu","doi":"10.17706/ijbbb.2022.12.2.39-42","DOIUrl":"https://doi.org/10.17706/ijbbb.2022.12.2.39-42","url":null,"abstract":": Covid - 19 virus has infected tens of millions of people since 2020. Its extremely high mortality rate has a huge impact on the development of the world. The influence of new coronavirus on the human body was discussed from two aspects: Antibody level and virus - cell attack. In addition, the study of the impact of the virus on the human body, expands the content of vaccine development and introduction. We can accurately study the relationship between the two through their structural differences, so as to have a good grasp of the structure of the vaccine.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83876910","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 : 2022-01-01DOI: 10.17706/ijbbb.2022.12.1.1-13
X. Ji
Drug-induced liver injury (DILI) remains a primary reason for drug withdrawal from the market, often after large amounts of money have been invested and patients put at risk in clinical trials. In dealing with DILI, the current 2D models are not sufficient in predicting DILI, thereby resulting in DILI discovered in clinical trials and postmarket surveillance. In recent decades, organoid technology has gained much attention and interest. The self-organizing and self-renewing features of organoids has led to their application in disease modeling, regenerative and personalized medicine, as well as in toxicity testing. The emergence of organoid technology challenges current in vitro and in vivo toxicity testing models as it overcomes several drawbacks two dimensional (2D) traditional models face. This review discusses the use of induced human pluripotent stem cells (iPSC) to make liver organoids specifically. Among many sources to make liver organoids, iPSCs are the least invasive and can ensure reproducible productions of liver organoids which better recapitulates the human liver in vivo. This paper, in particular, looks at the potential of iPSC-derived liver organoids as an exclusive tool for liver toxicity testing, including liver organoid construction, functionality, hepatic biomarkers measured, commercial availability, and challenges.
{"title":"The Use of iPSC-Derived Liver Organoids as an Exclusive Toxicity Testing Tool","authors":"X. Ji","doi":"10.17706/ijbbb.2022.12.1.1-13","DOIUrl":"https://doi.org/10.17706/ijbbb.2022.12.1.1-13","url":null,"abstract":"Drug-induced liver injury (DILI) remains a primary reason for drug withdrawal from the market, often after large amounts of money have been invested and patients put at risk in clinical trials. In dealing with DILI, the current 2D models are not sufficient in predicting DILI, thereby resulting in DILI discovered in clinical trials and postmarket surveillance. In recent decades, organoid technology has gained much attention and interest. The self-organizing and self-renewing features of organoids has led to their application in disease modeling, regenerative and personalized medicine, as well as in toxicity testing. The emergence of organoid technology challenges current in vitro and in vivo toxicity testing models as it overcomes several drawbacks two dimensional (2D) traditional models face. This review discusses the use of induced human pluripotent stem cells (iPSC) to make liver organoids specifically. Among many sources to make liver organoids, iPSCs are the least invasive and can ensure reproducible productions of liver organoids which better recapitulates the human liver in vivo. This paper, in particular, looks at the potential of iPSC-derived liver organoids as an exclusive tool for liver toxicity testing, including liver organoid construction, functionality, hepatic biomarkers measured, commercial availability, and challenges.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"40 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79523112","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 : 2022-01-01DOI: 10.17706/ijbbb.2022.12.1.14-21
Rui Zhao
COVID-19 is a serious pandemic since spring 2020. Numbers of traditional herbal medicines have been applied to conquer the virus. Here, we underline the potential risk of using the herbal medicines, by reviewing the chemical properties and toxicology of carcinogenicity chemical entities, e.g. aristolochic acids, glycyrrhizinic acid, in the herbal remedies. We stress here that although traditional herbal remedies are beneficial to relieve the COVID-19 symptoms, they should not be considered as preventive medicine or overdosing.
{"title":"Risk of Using Traditional Herbal Medicine against COVID-19","authors":"Rui Zhao","doi":"10.17706/ijbbb.2022.12.1.14-21","DOIUrl":"https://doi.org/10.17706/ijbbb.2022.12.1.14-21","url":null,"abstract":"COVID-19 is a serious pandemic since spring 2020. Numbers of traditional herbal medicines have been applied to conquer the virus. Here, we underline the potential risk of using the herbal medicines, by reviewing the chemical properties and toxicology of carcinogenicity chemical entities, e.g. aristolochic acids, glycyrrhizinic acid, in the herbal remedies. We stress here that although traditional herbal remedies are beneficial to relieve the COVID-19 symptoms, they should not be considered as preventive medicine or overdosing.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"86 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2022-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74802282","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 : 2021-10-01DOI: 10.17706/ijbbb.2021.11.4.74-81
Haonan Tong, Hao Chen, Cranos M. Williams
Accumulation of -omics data allows us to analyze the coordination and cooperation of multiple genes involved in different biological processes. Gene regulatory networks (GRNs) are used to characterize the regulatory relationships between transcription factors and downstream genes involved in different biological processes. The secondary cell wall (SCW) formation is involved with many important biological processes in plants, such as stress defense, mechanical reinforcement, and the transportation of water and nutrients. We construct GRNs based on the time-series data of VND7-induced de novo SCW formation using multiple algorithms, and then evaluate each GRN model based on the MYB46 experimental validated regulation data. From the optimal GRN model, we not only identify 8 TFs that have been previously demonstrated as the master regulators of SCW formation, but also show 6 novel SCW regulators which include EGL3, DREB19, TCP14, BZIP61, RGA2, and a zinc-finger type TF. From further in silico annotation of the downstream genes that are regulated by these TFs, we find the shared transcriptional program between the SCW formation and the processes of photosynthesis and drought response. Overall, our work suggests a pipeline for reconstructing and analyzing GRN to pinpoint gene functions in biological processes.
{"title":"Gene Regulatory Network of Secondary Cell Wall Biosynthesis during VND7 Induced de novo Xylem Formation","authors":"Haonan Tong, Hao Chen, Cranos M. Williams","doi":"10.17706/ijbbb.2021.11.4.74-81","DOIUrl":"https://doi.org/10.17706/ijbbb.2021.11.4.74-81","url":null,"abstract":"Accumulation of -omics data allows us to analyze the coordination and cooperation of multiple genes involved in different biological processes. Gene regulatory networks (GRNs) are used to characterize the regulatory relationships between transcription factors and downstream genes involved in different biological processes. The secondary cell wall (SCW) formation is involved with many important biological processes in plants, such as stress defense, mechanical reinforcement, and the transportation of water and nutrients. We construct GRNs based on the time-series data of VND7-induced de novo SCW formation using multiple algorithms, and then evaluate each GRN model based on the MYB46 experimental validated regulation data. From the optimal GRN model, we not only identify 8 TFs that have been previously demonstrated as the master regulators of SCW formation, but also show 6 novel SCW regulators which include EGL3, DREB19, TCP14, BZIP61, RGA2, and a zinc-finger type TF. From further in silico annotation of the downstream genes that are regulated by these TFs, we find the shared transcriptional program between the SCW formation and the processes of photosynthesis and drought response. Overall, our work suggests a pipeline for reconstructing and analyzing GRN to pinpoint gene functions in biological processes.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"41 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73179912","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 : 2021-10-01DOI: 10.17706/ijbbb.2021.11.4.82-88
Le Thi Tuyet Trinh, M. Ketudat-Cairns, Chotika Gosalawit, A. Boontawan
The compositions of the medium for recombinant Pichia pastoris producing omega-3 fatty acid were determined for maximum biomass production using crude glycerol as a carbon source and ammonium salts as nitrogen sources. The optimization of the medium was done using Box-Behnken a design software with 3 factors, 3 levels, 1 response for an optimal level of crude glycerol, (NH4)2SO4, (NH4)2HPO4. The optimum medium condition was 40 g/L crude glycerol, 3 g/L (NH4)2SO4, and 7 g/L (NH4)2HPO4. The highest biomass in flasks cultivation after 7 days production was 6.064 g/L DCW and 0.1516 g biomass/ g crude glycerol.
{"title":"Optimization of Nitrogen Sources and Carbon Source for Recombinant Omega-3 Fatty Acid-Containing Biomass Production","authors":"Le Thi Tuyet Trinh, M. Ketudat-Cairns, Chotika Gosalawit, A. Boontawan","doi":"10.17706/ijbbb.2021.11.4.82-88","DOIUrl":"https://doi.org/10.17706/ijbbb.2021.11.4.82-88","url":null,"abstract":"The compositions of the medium for recombinant Pichia pastoris producing omega-3 fatty acid were determined for maximum biomass production using crude glycerol as a carbon source and ammonium salts as nitrogen sources. The optimization of the medium was done using Box-Behnken a design software with 3 factors, 3 levels, 1 response for an optimal level of crude glycerol, (NH4)2SO4, (NH4)2HPO4. The optimum medium condition was 40 g/L crude glycerol, 3 g/L (NH4)2SO4, and 7 g/L (NH4)2HPO4. The highest biomass in flasks cultivation after 7 days production was 6.064 g/L DCW and 0.1516 g biomass/ g crude glycerol.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"79 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91223656","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 : 2021-04-01DOI: 10.17706/IJBBB.2021.11.2.34-39
R. Huang
Metabolomics, the global study of metabolites within cells, biofluids, tissues or organisms, has drawn people’s attention in the recent years. As one of the most widely used analytical methods, Liquid Chromatography-Mass Spectrometry (LC-MS) is commonly used to perform metabolomic analysis. Suitable sample preparation method is needed prior LC separation. It is best to use minimal sample preparation for metabolomics analysis or at least as little as one can get away with considering the purposes of metabolome profiling. Next, identification and quantification of significantly changed metabolites are carried out, with the aim of correlating their changes with pathological states, or with the effect of external influencing factors such as drugs or contaminants. Applications of metabolomics are also presented in this paper through a number of published researches using such methods in cell culture, drug study, and diseases. Overall, we provide an objective description of the LC-MS-based metabolomics, and summarize its application in cell culture, drug study, and diseases.
{"title":"Application of Liquid Chromatography-Mass Spectrometry-Based Metabolomics in Cell Culture, Drug Study, and Diseases","authors":"R. Huang","doi":"10.17706/IJBBB.2021.11.2.34-39","DOIUrl":"https://doi.org/10.17706/IJBBB.2021.11.2.34-39","url":null,"abstract":"Metabolomics, the global study of metabolites within cells, biofluids, tissues or organisms, has drawn people’s attention in the recent years. As one of the most widely used analytical methods, Liquid Chromatography-Mass Spectrometry (LC-MS) is commonly used to perform metabolomic analysis. Suitable sample preparation method is needed prior LC separation. It is best to use minimal sample preparation for metabolomics analysis or at least as little as one can get away with considering the purposes of metabolome profiling. Next, identification and quantification of significantly changed metabolites are carried out, with the aim of correlating their changes with pathological states, or with the effect of external influencing factors such as drugs or contaminants. Applications of metabolomics are also presented in this paper through a number of published researches using such methods in cell culture, drug study, and diseases. Overall, we provide an objective description of the LC-MS-based metabolomics, and summarize its application in cell culture, drug study, and diseases.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"68 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75641664","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 : 2021-04-01DOI: 10.17706/IJBBB.2021.11.2.14-21
Chutian Guo
Major depression is one of the typical psychiatric diseases. When psychiatric disease occurs, the function of brain cells may be influenced by some intestinal microbiota, which provides a pathway for the development of antidepressant drugs. The research on the correlation between microbiota and antidepressant has become a key issue in the treatment of major depression. This work explores the cell type specific gene interaction between microbiota and antidepressant drugs and isolates some potentially important genes that can be targets of further investigation in the mechanisms of how depressive related behaviours occur and act. Our analysis provides a deeper demonstration of the interaction between antidepressant and microbiota compared to original study, by means of an effective genetic matrix and PLS model.
{"title":"Cell Type Specific Gene Interaction between Microbiota and Antidepressant Drugs","authors":"Chutian Guo","doi":"10.17706/IJBBB.2021.11.2.14-21","DOIUrl":"https://doi.org/10.17706/IJBBB.2021.11.2.14-21","url":null,"abstract":"Major depression is one of the typical psychiatric diseases. When psychiatric disease occurs, the function of brain cells may be influenced by some intestinal microbiota, which provides a pathway for the development of antidepressant drugs. The research on the correlation between microbiota and antidepressant has become a key issue in the treatment of major depression. This work explores the cell type specific gene interaction between microbiota and antidepressant drugs and isolates some potentially important genes that can be targets of further investigation in the mechanisms of how depressive related behaviours occur and act. Our analysis provides a deeper demonstration of the interaction between antidepressant and microbiota compared to original study, by means of an effective genetic matrix and PLS model.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"1 1","pages":"14-21"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75793240","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 : 2021-04-01DOI: 10.17706/IJBBB.2021.11.2.22-33
Anna Liu, Junmeng Yang, Tina Yuan, Yongsheng Bai
Single nucleotide variants (SNVs) are mutations in the DNA sequence of a gene that are responsible for a variety of genetic disorders. Exonic variants located in the coding region of a gene can be especially harmful to an organism when they alter the biological functions of proteins. In this study, we performed multiple functional annotations and sequence alignments to assess the impact of SNVs in coding regions of genes associated with intellectual disability (ID). Through bioinformatics analysis, we identified three significant motifs in the coding region of ACTB, PTPN11, and GNAO1 prioritized by our pipeline. Detailed examination of these three genes revealed that eight variant coordinates were located in the three motifs, two of which from ACTB are reported to be pathogenic by MISCAST and three from GNAO1 are reported likely pathogenic according to clinical significance from National Center for Biotechnology Information (NCBI). In particular, we discovered two novel SNVs located at chr16:56370698 and chr16:56370711 in GNAO1 that are highly likely to be pathogenic and possibly associated with ID. Overall, our results revealed the pathogenic roles of SNVs within coding regions of ID candidate genes. Future work is to automate this process through developing a bioinformatics software that can identify novel SNVs in coding regions responsible for various human diseases.
{"title":"Computational Identification of Novel Missense Variants in Coding Regions of Genes Associated with Intellectual Disability","authors":"Anna Liu, Junmeng Yang, Tina Yuan, Yongsheng Bai","doi":"10.17706/IJBBB.2021.11.2.22-33","DOIUrl":"https://doi.org/10.17706/IJBBB.2021.11.2.22-33","url":null,"abstract":"Single nucleotide variants (SNVs) are mutations in the DNA sequence of a gene that are responsible for a variety of genetic disorders. Exonic variants located in the coding region of a gene can be especially harmful to an organism when they alter the biological functions of proteins. In this study, we performed multiple functional annotations and sequence alignments to assess the impact of SNVs in coding regions of genes associated with intellectual disability (ID). Through bioinformatics analysis, we identified three significant motifs in the coding region of ACTB, PTPN11, and GNAO1 prioritized by our pipeline. Detailed examination of these three genes revealed that eight variant coordinates were located in the three motifs, two of which from ACTB are reported to be pathogenic by MISCAST and three from GNAO1 are reported likely pathogenic according to clinical significance from National Center for Biotechnology Information (NCBI). In particular, we discovered two novel SNVs located at chr16:56370698 and chr16:56370711 in GNAO1 that are highly likely to be pathogenic and possibly associated with ID. Overall, our results revealed the pathogenic roles of SNVs within coding regions of ID candidate genes. Future work is to automate this process through developing a bioinformatics software that can identify novel SNVs in coding regions responsible for various human diseases.","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"37 1","pages":"22-33"},"PeriodicalIF":0.0,"publicationDate":"2021-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84092705","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 : 2021-01-01DOI: 10.33545/26646536.2021.v3.i1a.22
Rahimova S A, B. R, Ganbarli A A
{"title":"Antioxidant activity of fruits of Cerasus vulgaris Mill. species in the area of Nakhchivan Autonomous Republic","authors":"Rahimova S A, B. R, Ganbarli A A","doi":"10.33545/26646536.2021.v3.i1a.22","DOIUrl":"https://doi.org/10.33545/26646536.2021.v3.i1a.22","url":null,"abstract":"","PeriodicalId":13816,"journal":{"name":"International Journal of Bioscience, Biochemistry and Bioinformatics","volume":"15 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82928521","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：