Pub Date : 2019-04-23DOI: 10.5772/INTECHOPEN.83470
Saurav Mallik, U. Maulik, Namrata Tomar, Tapas Bhadra, A. Mukhopadhyay, Ayan Mukherji
RNA interference (RNAi) and gene inactivation are extensively used biological terms in biomedical research. Two categories of small ribonucleic acid (RNA) molecules, viz ., microRNA (miRNA) and small interfering RNA (siRNA) are central to the RNAi. There are various kinds of algorithms developed related to RNAi and gene silencing. In this book chapter, we provided a comprehensive review of various machine learning and association rule mining algorithms developed to handle different biological problems such as detection of gene signature, biomarker, gene module, potentially disordered protein, differentially methylated region and many more. We also provided a comparative study of different well-known classifiers along with other used methods. In addition, we demonstrated the brief biological information regarding the immense biological challenges for gene activation as well as their advantages, disadvantages and possible thera- peutic strategies. Finally, our study helps the bioinformaticians to understand the overall immense idea in different research dimensions including several learning algorithms for the benevolent of the disease discovery.
{"title":"Machine Learning and Rule Mining Techniques in the Study of Gene Inactivation and RNA Interference","authors":"Saurav Mallik, U. Maulik, Namrata Tomar, Tapas Bhadra, A. Mukhopadhyay, Ayan Mukherji","doi":"10.5772/INTECHOPEN.83470","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.83470","url":null,"abstract":"RNA interference (RNAi) and gene inactivation are extensively used biological terms in biomedical research. Two categories of small ribonucleic acid (RNA) molecules, viz ., microRNA (miRNA) and small interfering RNA (siRNA) are central to the RNAi. There are various kinds of algorithms developed related to RNAi and gene silencing. In this book chapter, we provided a comprehensive review of various machine learning and association rule mining algorithms developed to handle different biological problems such as detection of gene signature, biomarker, gene module, potentially disordered protein, differentially methylated region and many more. We also provided a comparative study of different well-known classifiers along with other used methods. In addition, we demonstrated the brief biological information regarding the immense biological challenges for gene activation as well as their advantages, disadvantages and possible thera- peutic strategies. Finally, our study helps the bioinformaticians to understand the overall immense idea in different research dimensions including several learning algorithms for the benevolent of the disease discovery.","PeriodicalId":336265,"journal":{"name":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133998957","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 : 2019-02-06DOI: 10.5772/intechopen.84229
Aditi Singh
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9/ gRNA system on the other hand, is a unique, targeted genome-modification technique derived from prokaryotic immune system. The cutting edge research and technology advancements in recent years have enabled the CRISPR-Cas9 system to become a popular tool for introducing heritable, precised, insertions and deletions in the eukaryotic genome.
{"title":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","authors":"Aditi Singh","doi":"10.5772/intechopen.84229","DOIUrl":"https://doi.org/10.5772/intechopen.84229","url":null,"abstract":"The clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9/ gRNA system on the other hand, is a unique, targeted genome-modification technique derived from prokaryotic immune system. The cutting edge research and technology advancements in recent years have enabled the CRISPR-Cas9 system to become a popular tool for introducing heritable, precised, insertions and deletions in the eukaryotic genome.","PeriodicalId":336265,"journal":{"name":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116947225","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 identification of various targets such as bacteria, viruses, and other cells remains a prerequisite for point-of-care diagnostics and biotechnological applications. Nucleic acids, as encoding information for all forms of life, are excellent biomarkers for detecting patho- gens, hereditary diseases, and cancers. To date, many techniques have been developed to detect nucleic acids. However, most of them are based on polymerase chain reaction (PCR) technology. These methods are sensitive and robust, but they require expensive instruments and trained personnel. DNA strand displacement amplification is carried out under isothermal conditions and therefore does not need expensive instruments. It is simple, fast, sensitive, specific, and inexpensive. In this chapter, we introduce the prin- ciples, methods, and updated applications of DNA strand displacement technology in the detection of infectious diseases. We also discuss how robust, sensitive, and specific nucleic acid detection could be obtained when combined with the novel CRISPR/Cas system.
{"title":"Strand Displacement Amplification for Multiplex Detection of Nucleic Acids","authors":"Lingwen Zeng, Omar Mukama, Xuewen Lu, Shilin Cao, DonghaiLin","doi":"10.5772/INTECHOPEN.80687","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80687","url":null,"abstract":"The identification of various targets such as bacteria, viruses, and other cells remains a prerequisite for point-of-care diagnostics and biotechnological applications. Nucleic acids, as encoding information for all forms of life, are excellent biomarkers for detecting patho- gens, hereditary diseases, and cancers. To date, many techniques have been developed to detect nucleic acids. However, most of them are based on polymerase chain reaction (PCR) technology. These methods are sensitive and robust, but they require expensive instruments and trained personnel. DNA strand displacement amplification is carried out under isothermal conditions and therefore does not need expensive instruments. It is simple, fast, sensitive, specific, and inexpensive. In this chapter, we introduce the prin- ciples, methods, and updated applications of DNA strand displacement technology in the detection of infectious diseases. We also discuss how robust, sensitive, and specific nucleic acid detection could be obtained when combined with the novel CRISPR/Cas system.","PeriodicalId":336265,"journal":{"name":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","volume":"83 1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116684297","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 : 2018-11-05DOI: 10.5772/INTECHOPEN.80874
Deise Cagliari, E. A. D. Santos, N. Dias, G. Smagghe, M. Zotti
RNAi in crop protection can be achieved not only by plant-incorporated protectants through plant transformation (transgenic) but also by nontransformative strategies such as formulations of sprayable dsRNAs used as direct control agents, resistance fac- tor repressors, or developmental disruptors. Therefore, the RNAi-based biopesticides are expected to reach the market also in the form of nontransgenic strategies such as sprayable products, stem injection, root drenching, seed treatment, or powder/granule. While the delivery of dsRNA by transgenic expression is well established, it requires generations of crop plants and is costly, which may take years and delays for practical application, depending on the regulatory rules, plant transformability, genetic stabil- ity, and public acceptance of genetically modified crop species. DsRNA delivery as a nontransgenic approach was already published as a proof-of-concept work, so it is time to point out some directions on how the real potential for agriculture and crop protection is. phloem-feeding insects as and aphids, RNAs prove difficult to get into insect cell
{"title":"Nontransformative Strategies for RNAi in Crop Protection","authors":"Deise Cagliari, E. A. D. Santos, N. Dias, G. Smagghe, M. Zotti","doi":"10.5772/INTECHOPEN.80874","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80874","url":null,"abstract":"RNAi in crop protection can be achieved not only by plant-incorporated protectants through plant transformation (transgenic) but also by nontransformative strategies such as formulations of sprayable dsRNAs used as direct control agents, resistance fac- tor repressors, or developmental disruptors. Therefore, the RNAi-based biopesticides are expected to reach the market also in the form of nontransgenic strategies such as sprayable products, stem injection, root drenching, seed treatment, or powder/granule. While the delivery of dsRNA by transgenic expression is well established, it requires generations of crop plants and is costly, which may take years and delays for practical application, depending on the regulatory rules, plant transformability, genetic stabil- ity, and public acceptance of genetically modified crop species. DsRNA delivery as a nontransgenic approach was already published as a proof-of-concept work, so it is time to point out some directions on how the real potential for agriculture and crop protection is. phloem-feeding insects as and aphids, RNAs prove difficult to get into insect cell","PeriodicalId":336265,"journal":{"name":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","volume":"238 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121354382","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 : 2018-11-05DOI: 10.5772/INTECHOPEN.79642
A. Qattan
MicroRNAs (miRs) are a class of non-coding RNAs, approximately 20–25 nucleotides long, discovered in the nematode, Caenorhabditis elegans , in 1993. There are two primary categories of non-coding RNA (ncRNA): (1) short interfering RNAs (siRNA) and (2) microRNAs (miRs). In general, miRs control protein production via partially complementary binding of the mRNA 3′UTRs. Both siRNAs and miRNAs are critical regulators of developmental and homeostatic processes as well as disease pathogenesis. While the treatment of advanced stage breast cancer presents several challenges, the development of therapeutic resistance contributes to a high mortality rate. Dysregulation of miR expression has been implicated in progression of breast cancer disease. Moreover, miRs have been found to play a role in the development of drug resistance. In this context, one of the therapeutic potentials of miRNAs is the correlation of circulating miR levels with breast cancer progression stages and disease phenotypes. Secondly, researchers are investigat-ing novel delivery strategies for the substitution or silencing of ncRNAs involved in the disease. This chapter describes both the general miRNA mechanism of actions and the miRNAs related to breast cancer research. It is specifically designed for breast cancer researchers with expertise in gene delivery, clinicians, and clinical translational scientists.
{"title":"Gene Silencing Agents in Breast Cancer","authors":"A. Qattan","doi":"10.5772/INTECHOPEN.79642","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.79642","url":null,"abstract":"MicroRNAs (miRs) are a class of non-coding RNAs, approximately 20–25 nucleotides long, discovered in the nematode, Caenorhabditis elegans , in 1993. There are two primary categories of non-coding RNA (ncRNA): (1) short interfering RNAs (siRNA) and (2) microRNAs (miRs). In general, miRs control protein production via partially complementary binding of the mRNA 3′UTRs. Both siRNAs and miRNAs are critical regulators of developmental and homeostatic processes as well as disease pathogenesis. While the treatment of advanced stage breast cancer presents several challenges, the development of therapeutic resistance contributes to a high mortality rate. Dysregulation of miR expression has been implicated in progression of breast cancer disease. Moreover, miRs have been found to play a role in the development of drug resistance. In this context, one of the therapeutic potentials of miRNAs is the correlation of circulating miR levels with breast cancer progression stages and disease phenotypes. Secondly, researchers are investigat-ing novel delivery strategies for the substitution or silencing of ncRNAs involved in the disease. This chapter describes both the general miRNA mechanism of actions and the miRNAs related to breast cancer research. It is specifically designed for breast cancer researchers with expertise in gene delivery, clinicians, and clinical translational scientists.","PeriodicalId":336265,"journal":{"name":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","volume":"110 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131353183","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 : 2018-11-05DOI: 10.5772/INTECHOPEN.80245
M. Sánchez-Martín, I. García-Tuñón
Genome-editing nucleases like the popular CRISPR/Cas9 enable the generation of knock- out cell lines and null zygotes by inducing site-specific double-stranded breaks (DSBs) within a genome. In most cases, when a DNA template is not present, the DSB is repaired by nonhomologous end joining (NHEJ), resulting in small nucleotide insertions or dele tions that can be used to construct knockout alleles. However, for several reasons, these mutations do not produce the desired null result in all cases, instead generating a similar protein with functional activity. This undesirable effect could limit the therapeutic effi - ciency of gene therapy strategies focused on abrogating oncogene expression by CRISPR/ Cas9 and should be taken into account. This chapter reviews the irruption of CRISPR technology for gene silencing and its application in gene therapy.
{"title":"CRISPR-ERA for Switching Off (Onco) Genes","authors":"M. Sánchez-Martín, I. García-Tuñón","doi":"10.5772/INTECHOPEN.80245","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80245","url":null,"abstract":"Genome-editing nucleases like the popular CRISPR/Cas9 enable the generation of knock- out cell lines and null zygotes by inducing site-specific double-stranded breaks (DSBs) within a genome. In most cases, when a DNA template is not present, the DSB is repaired by nonhomologous end joining (NHEJ), resulting in small nucleotide insertions or dele tions that can be used to construct knockout alleles. However, for several reasons, these mutations do not produce the desired null result in all cases, instead generating a similar protein with functional activity. This undesirable effect could limit the therapeutic effi - ciency of gene therapy strategies focused on abrogating oncogene expression by CRISPR/ Cas9 and should be taken into account. This chapter reviews the irruption of CRISPR technology for gene silencing and its application in gene therapy.","PeriodicalId":336265,"journal":{"name":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130064226","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 : 2018-11-05DOI: 10.5772/INTECHOPEN.80775
Takeshi Yasuda, Katsushi Tajima
The clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 method is a powerful tool for genome editing, by introducing a DNA double-strand break (DSB) at the specific site. The gene knock-out can be achieved by the deletion or inser - tion at the CRISPR/Cas9-mediated DSB site by error-prone nonhomologous end joining repair in targeted cells. However, the gene knock-in is still difficult as compared to the knock-out, because of the low efficiency of homology directed repair with donor DNA in cells. Therefore, to efficiently select the knock-in cells, we developed a complicated donor DNA plasmid containing an antibiotic-resistance gene, in addition to the knock-in sequence and the two homology arms. MultiSite Gateway technology is a useful tool for constructing this complicated plasmid. We describe the MultiSite Gateway technology and provide an overview of the DSB repair pathways to clarify the knock-out and knock- in methods by the CRISPR/Cas9 system.
{"title":"MultiSite Gateway Technology Is Useful for Donor DNA Plasmid Construction in CRISPR/Cas9-Mediated Knock-In System","authors":"Takeshi Yasuda, Katsushi Tajima","doi":"10.5772/INTECHOPEN.80775","DOIUrl":"https://doi.org/10.5772/INTECHOPEN.80775","url":null,"abstract":"The clustered regulatory interspaced short palindromic repeats (CRISPR)/Cas9 method is a powerful tool for genome editing, by introducing a DNA double-strand break (DSB) at the specific site. The gene knock-out can be achieved by the deletion or inser - tion at the CRISPR/Cas9-mediated DSB site by error-prone nonhomologous end joining repair in targeted cells. However, the gene knock-in is still difficult as compared to the knock-out, because of the low efficiency of homology directed repair with donor DNA in cells. Therefore, to efficiently select the knock-in cells, we developed a complicated donor DNA plasmid containing an antibiotic-resistance gene, in addition to the knock-in sequence and the two homology arms. MultiSite Gateway technology is a useful tool for constructing this complicated plasmid. We describe the MultiSite Gateway technology and provide an overview of the DSB repair pathways to clarify the knock-out and knock- in methods by the CRISPR/Cas9 system.","PeriodicalId":336265,"journal":{"name":"Modulating Gene Expression - Abridging the RNAi and CRISPR-Cas9 Technologies","volume":"83 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2018-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128679283","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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