This document discusses RNA interference (RNAi), a biological mechanism that leads to post-transcriptional gene silencing triggered by double-stranded RNA molecules. It was discovered in 1998 by Fire and Mello, who received the Nobel Prize for this work. The mechanism involves double-stranded RNA being processed by the enzyme Dicer into small interfering RNAs that integrate into the RNA-induced silencing complex and guide mRNA degradation. RNAi can be induced by synthetic siRNAs or endogenous microRNAs and represents a powerful tool for studying gene function and developing therapies.
Micro RNARNA INTERFERENCE AND ITS APPLICATIONS IN CROP IMPROVE...SANIVARAPUNAGALAKSHM
This document provides an overview of RNA interference (RNAi) and its applications in crop improvement. It discusses the history and discovery of RNAi, the mechanism of RNAi involving initiation by Dicer and effector function of RISC complexes, and methods of transforming plants with RNAi constructs. Applications of RNAi described in the document include modifying traits in rice, maize, barley, cotton, jute, tomato, lathyris, and coffee to improve nutritional quality, increase yields, confer virus resistance, and remove toxic compounds.
Gene silencing and its application in crop improvementVINOD BARPA
Gene silencing is describing as epigenetic processes of gene regulation. Gene silencing is a technique used to turn down or switch off the activity of genes by a mechanism other than genetic modification. That is, a gene which would be expressed (turned on) under normal circumstances is switched off by machinery in the cell.
Gene silencing (GS) is defined as a molecular process involved in the down regulation of specific genes, the mechanisms of Gene silencing that suppress gene activity in plants has extended that control of gene expression. Currently, there are several routes of GS identified in plants, such as: transcriptional gene silencing and post transcriptional (PTGS or RNAi) gene silencing (Fire et al. 1998), microRNA silencing and virus induced gene silencing. All these pathways play an important role at the cellular level, affecting gene regulation and protection against viruses and transposons. The post-transcriptional gene silencing involves breakdown of the mRNA itself by various techniques like Ribozymes, antisense RNA, DNAzymes and RNA interference (RNAi). Among all these techniques RNA interference has emerged as most potent tool to effect targeted gene silencing and is being used to determine the function of genes which are expressed in a constitutive or cell-fate dependent manner.
This document provides an overview of RNA interference (RNAi) including its mechanism, applications, and methods for delivering small interfering RNA (siRNA). It discusses how dsRNA is processed by the enzyme Dicer into siRNAs which are incorporated into the RISC complex to degrade complementary mRNA. Viral vectors, liposomes, nanoparticles, and chemical modifications are described as methods used to deliver exogenous siRNAs. The document outlines both the therapeutic potential of RNAi and challenges associated with effective siRNA delivery.
RNA interference is a phenomenon where RNA molecules inhibit gene expression or translation. It was discovered in 1998 by Fire and Mello, who showed that double-stranded RNA silences or interferes with the expression of homologous genes more efficiently than single-stranded RNA. This led to the discovery of microRNAs and small interfering RNAs that are key players in RNA interference. RNA interference is now used in applications ranging from altering crop traits to exploring gene function and generating disease-resistant plants.
This presentation provides an overview of RNA interference (RNAi) including its history, components, mechanism, advantages, and applications. It discusses how RNAi involves long double-stranded RNAs being cut by the enzyme Dicer into short interfering RNAs (siRNAs) that then guide the RNA-induced silencing complex (RISC) to degrade messenger RNAs with complementary base sequences, preventing gene expression. The presentation also compares siRNAs and microRNAs (miRNAs), noting similarities in their biogenesis and roles in post-transcriptional gene silencing, while distinguishing their origins, sizes, targets, and effects on mRNA. Recent applications of RNAi modulation of viral replication and gene expression are highlighted.
Antisense RNA Technology for crop improvement.pptxSanyamPatel2
This document summarizes a study that used antisense RNA technology to improve the nutritional content of crops. It discusses how researchers used RNA interference to suppress specific genes involved in lysine catabolism and carotenoid biosynthesis in maize and tomato, respectively. By targeting these genes, they were able to increase the levels of lysine and carotenoids in the crops. The studies demonstrate how antisense RNA technology can be applied to genetically modify crops for improved nutritional qualities.
This document provides an overview of RNA interference (RNAi), including its definition, mechanism, generation of small interfering RNA, delivery methods, and applications. RNAi is a conserved mechanism in eukaryotes where double-stranded RNA is cut into small interfering RNA by the enzyme Dicer. These siRNAs then bind to complementary mRNA and induce its degradation via the RNA-induced silencing complex. The document discusses the key components of RNAi, differences between siRNAs and microRNAs, generation of siRNAs, challenges with siRNA delivery, and applications of RNAi technology in areas like cancer treatment, stem cell research, and infectious disease.
This document discusses RNA interference (RNAi), a biological mechanism that leads to post-transcriptional gene silencing triggered by double-stranded RNA molecules. It was discovered in 1998 by Fire and Mello, who received the Nobel Prize for this work. The mechanism involves double-stranded RNA being processed by the enzyme Dicer into small interfering RNAs that integrate into the RNA-induced silencing complex and guide mRNA degradation. RNAi can be induced by synthetic siRNAs or endogenous microRNAs and represents a powerful tool for studying gene function and developing therapies.
Micro RNARNA INTERFERENCE AND ITS APPLICATIONS IN CROP IMPROVE...SANIVARAPUNAGALAKSHM
This document provides an overview of RNA interference (RNAi) and its applications in crop improvement. It discusses the history and discovery of RNAi, the mechanism of RNAi involving initiation by Dicer and effector function of RISC complexes, and methods of transforming plants with RNAi constructs. Applications of RNAi described in the document include modifying traits in rice, maize, barley, cotton, jute, tomato, lathyris, and coffee to improve nutritional quality, increase yields, confer virus resistance, and remove toxic compounds.
Gene silencing and its application in crop improvementVINOD BARPA
Gene silencing is describing as epigenetic processes of gene regulation. Gene silencing is a technique used to turn down or switch off the activity of genes by a mechanism other than genetic modification. That is, a gene which would be expressed (turned on) under normal circumstances is switched off by machinery in the cell.
Gene silencing (GS) is defined as a molecular process involved in the down regulation of specific genes, the mechanisms of Gene silencing that suppress gene activity in plants has extended that control of gene expression. Currently, there are several routes of GS identified in plants, such as: transcriptional gene silencing and post transcriptional (PTGS or RNAi) gene silencing (Fire et al. 1998), microRNA silencing and virus induced gene silencing. All these pathways play an important role at the cellular level, affecting gene regulation and protection against viruses and transposons. The post-transcriptional gene silencing involves breakdown of the mRNA itself by various techniques like Ribozymes, antisense RNA, DNAzymes and RNA interference (RNAi). Among all these techniques RNA interference has emerged as most potent tool to effect targeted gene silencing and is being used to determine the function of genes which are expressed in a constitutive or cell-fate dependent manner.
This document provides an overview of RNA interference (RNAi) including its mechanism, applications, and methods for delivering small interfering RNA (siRNA). It discusses how dsRNA is processed by the enzyme Dicer into siRNAs which are incorporated into the RISC complex to degrade complementary mRNA. Viral vectors, liposomes, nanoparticles, and chemical modifications are described as methods used to deliver exogenous siRNAs. The document outlines both the therapeutic potential of RNAi and challenges associated with effective siRNA delivery.
RNA interference is a phenomenon where RNA molecules inhibit gene expression or translation. It was discovered in 1998 by Fire and Mello, who showed that double-stranded RNA silences or interferes with the expression of homologous genes more efficiently than single-stranded RNA. This led to the discovery of microRNAs and small interfering RNAs that are key players in RNA interference. RNA interference is now used in applications ranging from altering crop traits to exploring gene function and generating disease-resistant plants.
This presentation provides an overview of RNA interference (RNAi) including its history, components, mechanism, advantages, and applications. It discusses how RNAi involves long double-stranded RNAs being cut by the enzyme Dicer into short interfering RNAs (siRNAs) that then guide the RNA-induced silencing complex (RISC) to degrade messenger RNAs with complementary base sequences, preventing gene expression. The presentation also compares siRNAs and microRNAs (miRNAs), noting similarities in their biogenesis and roles in post-transcriptional gene silencing, while distinguishing their origins, sizes, targets, and effects on mRNA. Recent applications of RNAi modulation of viral replication and gene expression are highlighted.
Antisense RNA Technology for crop improvement.pptxSanyamPatel2
This document summarizes a study that used antisense RNA technology to improve the nutritional content of crops. It discusses how researchers used RNA interference to suppress specific genes involved in lysine catabolism and carotenoid biosynthesis in maize and tomato, respectively. By targeting these genes, they were able to increase the levels of lysine and carotenoids in the crops. The studies demonstrate how antisense RNA technology can be applied to genetically modify crops for improved nutritional qualities.
This document provides an overview of RNA interference (RNAi), including its definition, mechanism, generation of small interfering RNA, delivery methods, and applications. RNAi is a conserved mechanism in eukaryotes where double-stranded RNA is cut into small interfering RNA by the enzyme Dicer. These siRNAs then bind to complementary mRNA and induce its degradation via the RNA-induced silencing complex. The document discusses the key components of RNAi, differences between siRNAs and microRNAs, generation of siRNAs, challenges with siRNA delivery, and applications of RNAi technology in areas like cancer treatment, stem cell research, and infectious disease.
Gene silencing is a technique that reduces or eliminates protein production from a gene. It occurs through RNA interference, where small interfering RNAs are processed by an enzyme called Dicer and loaded into an RNA-induced silencing complex (RISC) that targets complementary mRNAs for degradation. There are two main types of gene silencing - transcriptional which alters DNA accessibility, and post-transcriptional via RNAi technologies. RNAi has therapeutic applications for cancer, infectious diseases, and neurodegenerative disorders by knocking down target genes. The first approved RNAi drug, Patisiran, treats hereditary transthyretin-mediated amyloidosis.
RNA interference (RNAi) is a mechanism that inhibits gene expression through degradation of mRNA. It was discovered in 1998 when researchers found that injecting double-stranded RNA into worms caused specific gene silencing. The mechanism involves dicer enzymes cutting double-stranded RNA into small interfering RNAs (siRNAs) which are incorporated into the RNA-induced silencing complex (RISC) and guide it to degrade complementary mRNA targets. siRNAs can be designed to target specific genes and various delivery methods exist to introduce siRNAs into cells and organisms. RNAi has applications in research, therapeutics, and agriculture by allowing targeted gene silencing.
Gene silencing is the regulation of gene expression in a cell to prevent the expression of a certain gene. Gene silencing can occur during either transcription or translation and is often used in research.
This document summarizes a seminar presentation on antisense RNA technology. The presentation covered:
1. The introduction defined antisense RNA and its potential for crop improvement to meet rising global food demand.
2. The mechanisms of antisense RNA technology were explained, including how antisense RNA binds to mRNA to inhibit translation and activate RNase H degradation.
3. The history of antisense technology was discussed, including its first observation in nature's HOK/SOK system and early experiments in the 1990s that helped define gene silencing.
Gene silencing is a mechanism of gene regulation that switches off genes without genetic modification. It can occur at the transcriptional or post-transcriptional level. Post-transcriptional gene silencing is achieved through antisense technology or RNA interference (RNAi). Antisense technology uses synthetic nucleic acid molecules that are complementary to mRNA to block translation into proteins. RNAi involves introducing double-stranded RNA that is processed into small interfering RNAs (siRNAs) that guide the RNA-induced silencing complex (RISC) to degrade mRNAs with complementary sequences, thereby silencing genes. Both antisense technology and RNAi have applications for treating diseases and studying gene function and regulation.
RNA interference (RNAi) is a mechanism where double-stranded RNA inhibits gene expression. It was discovered in plants, fungi, and animals. The mechanism involves dicer enzymes cleaving long double-stranded RNA into short interfering RNAs (siRNAs). These siRNAs are incorporated into an RNA-induced silencing complex (RISC) which guides the complex to mRNAs with complementary sequences, resulting in their degradation. RNAi has applications in therapeutics for cancer, viruses, and genetic disorders, as well as research in gene function and pathways.
This document discusses small interfering RNA (siRNA), which are double stranded RNA molecules that play a role in RNA interference (RNAi) pathways by interfering with gene expression of complementary nucleotide sequences. siRNAs are naturally produced by the enzyme Dicer but can also be artificially introduced. The document provides details on siRNA structure, the RNAi mechanism, guidelines for effective siRNA design, methods of siRNA synthesis, delivery methods, and applications in gene silencing research and potential therapies.
MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two important types of noncoding RNAs that regulate gene expression. miRNAs are 22 nucleotides on average that silence target mRNAs through base pairing with RNA-induced silencing complex (RISC). lncRNAs modulate genes in various ways, such as restricting polymerase access or facilitating transcription factor binding. Both miRNAs and lncRNAs play critical roles in development and disease, with miRNAs receiving the 2006 Nobel Prize for their discovery.
Gene silencing is a technique that aims to reduce or eliminate the production of a protein from its corresponding gene. There are two main types of gene silencing: transcriptional gene silencing which occurs at the transcriptional level through histone modifications or DNA methylation, and post-transcriptional gene silencing which occurs after transcription through RNA interference (RNAi) or microRNA (miRNA) pathways. Gene silencing has many applications including cancer treatment, biotechnology, and studying gene function.
Gene silencing is a technique that reduces or eliminates the production of a protein from its corresponding gene through mechanisms other than genetic modification. There are two main types of gene silencing - transcriptional and post-transcriptional. Post-transcriptional gene silencing includes RNA interference (RNAi), which involves introducing double-stranded RNA that binds to mRNA and prevents replication, effectively silencing gene expression in a sequence-specific manner. RNAi is a powerful tool for gene function analysis and applications in biotechnology and agriculture.
This document provides an overview of RNA silencing in plants. It discusses that RNA silencing refers to gene silencing by non-coding RNAs like microRNAs. The mechanism involves double-stranded RNA being processed by an enzyme into small RNAs that guide silencing. There are multiple pathways of RNA silencing in plants, including the microRNA, trans-acting small interfering RNA, RNA-directed DNA methylation, and exogenic RNA pathways. The document also discusses applications of RNA silencing technologies in plants for resistance to stresses and altering traits, as well as advantages and disadvantages.
Gene silencing is a process by which gene expression is regulated without modifying the genetic sequence. It occurs through transcriptional or post-transcriptional mechanisms. RNA interference (RNAi) is a major method of post-transcriptional gene silencing where double-stranded RNA introduced into a cell leads to degradation of mRNA from complementary genes. RNAi has various applications including cancer treatment by targeting oncogenes, inhibiting HIV replication, and improving crops by reducing undesirable compounds.
This document discusses RNA interference (RNAi) and antisense RNA technology for controlling gene expression in plants. It explains that RNAi works by introducing double-stranded RNA that is processed into siRNAs to target and degrade complementary mRNA, preventing protein production. Antisense RNA also binds to mRNA but blocks processing or translation. Both techniques allow specific genes to be silenced and have applications for improving plant traits like disease resistance, ripening time, and nutrient content. The document provides detailed explanations of the mechanisms and applications of RNAi and antisense RNA technology.
Antisense RNA technology & its role in crop improvement ppt surendra singhDrSurendraSingh2
This document discusses antisense RNA technology and its role in crop improvement. It begins by introducing antisense RNA as a method for inhibiting gene expression through complementary base pairing. It then discusses various applications of antisense RNA technology in crop improvement, including delaying fruit ripening in tomato and flower senescence in carnation, producing male sterility in petunia, and reducing neurotoxins in crops like khesari. The document concludes by noting that antisense RNA technology is an efficient gene knockdown method that could be useful for genetic improvement in many plant species.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Gene silencing, also known as post-transcriptional gene silencing (PTGS), occurs when a gene is switched off by mechanisms other than mutation. It was first observed when an attempt to overexpress a pigment gene in petunia resulted in loss of pigment. This was due to co-suppression of both the endogenous gene and transgene. PTGS can occur via transcriptional gene silencing (TGS) or post-transcriptional gene silencing (PTGS) where mRNA is degraded. PTGS involves double-stranded RNA triggering cleavage and degradation of homologous mRNA through the RNA interference (RNAi) pathway, which involves dicer, siRNAs, and RISC complex.
RNAi interuption mechanism and applicationSumeena Karki
RNA interference is a natural mechanism that inhibits gene expression. It was first discovered accidentally in 1990 when researchers trying to increase pigmentation in petunias found that introduced homologous RNA led to less pigmentation. Further work found similar mechanisms in plants and fungi termed cosuppression and quelling. Craig Mello and Andrew Fire's 1998 paper demonstrating gene silencing in C. elegans using double stranded RNA led to the coining of the term RNAi. The mechanism involves Dicer and Drosha enzymes processing trigger RNA into siRNAs which are loaded into the RISC complex containing Argonaute proteins to degrade complementary mRNA, silencing gene expression. RNAi plays roles in gene regulation, genome stability, and provides therapeutic tools for disease
RNA interference (RNAi) is a biological mechanism that leads to post-transcriptional gene silencing triggered by double-stranded RNA (dsRNA) molecules. It involves small interfering RNAs (siRNAs) and microRNAs (miRNAs) that are processed by Dicer nuclease and loaded into an RNA-induced silencing complex (RISC) which targets and degrades messenger RNAs (mRNAs). The mechanism of RNAi involves dsRNA being cleaved by Dicer into siRNAs which are incorporated into RISC and used as a guide to degrade complementary mRNAs. RNAi has various applications in crop improvement traits like enhanced shelf life, male sterility/fertility, biofortification, aller
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
Gene silencing is a technique that reduces or eliminates protein production from a gene. It occurs through RNA interference, where small interfering RNAs are processed by an enzyme called Dicer and loaded into an RNA-induced silencing complex (RISC) that targets complementary mRNAs for degradation. There are two main types of gene silencing - transcriptional which alters DNA accessibility, and post-transcriptional via RNAi technologies. RNAi has therapeutic applications for cancer, infectious diseases, and neurodegenerative disorders by knocking down target genes. The first approved RNAi drug, Patisiran, treats hereditary transthyretin-mediated amyloidosis.
RNA interference (RNAi) is a mechanism that inhibits gene expression through degradation of mRNA. It was discovered in 1998 when researchers found that injecting double-stranded RNA into worms caused specific gene silencing. The mechanism involves dicer enzymes cutting double-stranded RNA into small interfering RNAs (siRNAs) which are incorporated into the RNA-induced silencing complex (RISC) and guide it to degrade complementary mRNA targets. siRNAs can be designed to target specific genes and various delivery methods exist to introduce siRNAs into cells and organisms. RNAi has applications in research, therapeutics, and agriculture by allowing targeted gene silencing.
Gene silencing is the regulation of gene expression in a cell to prevent the expression of a certain gene. Gene silencing can occur during either transcription or translation and is often used in research.
This document summarizes a seminar presentation on antisense RNA technology. The presentation covered:
1. The introduction defined antisense RNA and its potential for crop improvement to meet rising global food demand.
2. The mechanisms of antisense RNA technology were explained, including how antisense RNA binds to mRNA to inhibit translation and activate RNase H degradation.
3. The history of antisense technology was discussed, including its first observation in nature's HOK/SOK system and early experiments in the 1990s that helped define gene silencing.
Gene silencing is a mechanism of gene regulation that switches off genes without genetic modification. It can occur at the transcriptional or post-transcriptional level. Post-transcriptional gene silencing is achieved through antisense technology or RNA interference (RNAi). Antisense technology uses synthetic nucleic acid molecules that are complementary to mRNA to block translation into proteins. RNAi involves introducing double-stranded RNA that is processed into small interfering RNAs (siRNAs) that guide the RNA-induced silencing complex (RISC) to degrade mRNAs with complementary sequences, thereby silencing genes. Both antisense technology and RNAi have applications for treating diseases and studying gene function and regulation.
RNA interference (RNAi) is a mechanism where double-stranded RNA inhibits gene expression. It was discovered in plants, fungi, and animals. The mechanism involves dicer enzymes cleaving long double-stranded RNA into short interfering RNAs (siRNAs). These siRNAs are incorporated into an RNA-induced silencing complex (RISC) which guides the complex to mRNAs with complementary sequences, resulting in their degradation. RNAi has applications in therapeutics for cancer, viruses, and genetic disorders, as well as research in gene function and pathways.
This document discusses small interfering RNA (siRNA), which are double stranded RNA molecules that play a role in RNA interference (RNAi) pathways by interfering with gene expression of complementary nucleotide sequences. siRNAs are naturally produced by the enzyme Dicer but can also be artificially introduced. The document provides details on siRNA structure, the RNAi mechanism, guidelines for effective siRNA design, methods of siRNA synthesis, delivery methods, and applications in gene silencing research and potential therapies.
MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs) are two important types of noncoding RNAs that regulate gene expression. miRNAs are 22 nucleotides on average that silence target mRNAs through base pairing with RNA-induced silencing complex (RISC). lncRNAs modulate genes in various ways, such as restricting polymerase access or facilitating transcription factor binding. Both miRNAs and lncRNAs play critical roles in development and disease, with miRNAs receiving the 2006 Nobel Prize for their discovery.
Gene silencing is a technique that aims to reduce or eliminate the production of a protein from its corresponding gene. There are two main types of gene silencing: transcriptional gene silencing which occurs at the transcriptional level through histone modifications or DNA methylation, and post-transcriptional gene silencing which occurs after transcription through RNA interference (RNAi) or microRNA (miRNA) pathways. Gene silencing has many applications including cancer treatment, biotechnology, and studying gene function.
Gene silencing is a technique that reduces or eliminates the production of a protein from its corresponding gene through mechanisms other than genetic modification. There are two main types of gene silencing - transcriptional and post-transcriptional. Post-transcriptional gene silencing includes RNA interference (RNAi), which involves introducing double-stranded RNA that binds to mRNA and prevents replication, effectively silencing gene expression in a sequence-specific manner. RNAi is a powerful tool for gene function analysis and applications in biotechnology and agriculture.
This document provides an overview of RNA silencing in plants. It discusses that RNA silencing refers to gene silencing by non-coding RNAs like microRNAs. The mechanism involves double-stranded RNA being processed by an enzyme into small RNAs that guide silencing. There are multiple pathways of RNA silencing in plants, including the microRNA, trans-acting small interfering RNA, RNA-directed DNA methylation, and exogenic RNA pathways. The document also discusses applications of RNA silencing technologies in plants for resistance to stresses and altering traits, as well as advantages and disadvantages.
Gene silencing is a process by which gene expression is regulated without modifying the genetic sequence. It occurs through transcriptional or post-transcriptional mechanisms. RNA interference (RNAi) is a major method of post-transcriptional gene silencing where double-stranded RNA introduced into a cell leads to degradation of mRNA from complementary genes. RNAi has various applications including cancer treatment by targeting oncogenes, inhibiting HIV replication, and improving crops by reducing undesirable compounds.
This document discusses RNA interference (RNAi) and antisense RNA technology for controlling gene expression in plants. It explains that RNAi works by introducing double-stranded RNA that is processed into siRNAs to target and degrade complementary mRNA, preventing protein production. Antisense RNA also binds to mRNA but blocks processing or translation. Both techniques allow specific genes to be silenced and have applications for improving plant traits like disease resistance, ripening time, and nutrient content. The document provides detailed explanations of the mechanisms and applications of RNAi and antisense RNA technology.
Antisense RNA technology & its role in crop improvement ppt surendra singhDrSurendraSingh2
This document discusses antisense RNA technology and its role in crop improvement. It begins by introducing antisense RNA as a method for inhibiting gene expression through complementary base pairing. It then discusses various applications of antisense RNA technology in crop improvement, including delaying fruit ripening in tomato and flower senescence in carnation, producing male sterility in petunia, and reducing neurotoxins in crops like khesari. The document concludes by noting that antisense RNA technology is an efficient gene knockdown method that could be useful for genetic improvement in many plant species.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Gene silencing, also known as post-transcriptional gene silencing (PTGS), occurs when a gene is switched off by mechanisms other than mutation. It was first observed when an attempt to overexpress a pigment gene in petunia resulted in loss of pigment. This was due to co-suppression of both the endogenous gene and transgene. PTGS can occur via transcriptional gene silencing (TGS) or post-transcriptional gene silencing (PTGS) where mRNA is degraded. PTGS involves double-stranded RNA triggering cleavage and degradation of homologous mRNA through the RNA interference (RNAi) pathway, which involves dicer, siRNAs, and RISC complex.
RNAi interuption mechanism and applicationSumeena Karki
RNA interference is a natural mechanism that inhibits gene expression. It was first discovered accidentally in 1990 when researchers trying to increase pigmentation in petunias found that introduced homologous RNA led to less pigmentation. Further work found similar mechanisms in plants and fungi termed cosuppression and quelling. Craig Mello and Andrew Fire's 1998 paper demonstrating gene silencing in C. elegans using double stranded RNA led to the coining of the term RNAi. The mechanism involves Dicer and Drosha enzymes processing trigger RNA into siRNAs which are loaded into the RISC complex containing Argonaute proteins to degrade complementary mRNA, silencing gene expression. RNAi plays roles in gene regulation, genome stability, and provides therapeutic tools for disease
RNA interference (RNAi) is a biological mechanism that leads to post-transcriptional gene silencing triggered by double-stranded RNA (dsRNA) molecules. It involves small interfering RNAs (siRNAs) and microRNAs (miRNAs) that are processed by Dicer nuclease and loaded into an RNA-induced silencing complex (RISC) which targets and degrades messenger RNAs (mRNAs). The mechanism of RNAi involves dsRNA being cleaved by Dicer into siRNAs which are incorporated into RISC and used as a guide to degrade complementary mRNAs. RNAi has various applications in crop improvement traits like enhanced shelf life, male sterility/fertility, biofortification, aller
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Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
Current Ms word generated power point presentation covers major details about the micronuclei test. It's significance and assays to conduct it. It is used to detect the micronuclei formation inside the cells of nearly every multicellular organism. It's formation takes place during chromosomal sepration at metaphase.
ESPP presentation to EU Waste Water Network, 4th June 2024 “EU policies driving nutrient removal and recycling
and the revised UWWTD (Urban Waste Water Treatment Directive)”
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
2. Gene silencing
Interruption or suppression of the expression of a gene at transcriptional or translational levels.
Two classes:
• Transcriptional Gene silencing
• Post Transcriptional gene silencing
Post-transcriptional gene silencing (PTGS) is a mechanism that degrades specific messenger RNAs and thereby
reduces the expression of a specific gene.
PTGS has many names:
• Co-suppression in plants,
• Quelling in fungi
• and RNA interference (RNAi) in animals,
In all cases, mRNA is degraded to decrease gene expression.
The process is homology dependant
PTGS mechanisms naturally occur in organisms
3. PTGS can be artificially induced by the introduction of double-stranded RNA (dsRNA)
• A potent tool in functional genomics
• Is used as a tool to knock down expression of specific genes in a variety of organisms
• Therapeutic applications in cancer, infectious diseases and neurodegenerative diseases
History
Co-suppression was observed for the first time in petunias.
In a Genetic Engineering experiment, Rich Jorgensen and colleagues in1990 introduced pigment-producing genes
under the control of a powerful promoter into petunia plants
The genes introduced were chalcone synthase ChsA transgene or a dihydroflavonol-4-reductase transgene.Both
genes encoded proteins involved in the production of anthocyanin pigments.
The intention was to deepen the purple colour of petunia flowers. However many flowers appeared variegated
or even white
Jorgensen named the observed phenomenon "cosuppression", since the expression of both the introduced gene
and the homologous endogenous gene was suppressed
4.
5. RNA –I
Fire and Mello first injected dsRNA — a mixture of both sense and antisense strands — into C. elegans.
The investigators injected dsRNA corresponding to a 742-nucleotide segment of unc22 gene into either the
gonad or body cavity region of an adult nematode
unc22 encodes an abundant but nonessential myofilament protein, and the decrease in unc22 activity is
supposed to produce an increasingly severe twitching phenotype
The injected animal showed weak twitching, whereas the progeny individuals were strong twitchers.
Thus it was shown that exogenous introduction of dsRNA corresponding to a gene could result in silencing of
the endogenous gene
The injection resulted in much more efficient silencing than injection of either the sense or the antisense strands
alone. Indeed, injection of just a few molecules of dsRNA per cell was sufficient to completely silence the
homologous gene's expression.
Furthermore, injection of dsRNA into the gut of the worm caused gene silencing not only throughout the worm,
but also in its first generation offspring
This process, of PTGS by the introduction of dS RNA was named RNA interference
6. FEATURES OF RNA-I
• Features of the RNA-i mechanism are:
• The process is initiated by the dsRNA,
• The target RNA is degraded in a homology dependent fashion, and
• The degradative machinery requires a set of proteins which are similar in structure and function across
most organisms
In most of these processes, certain invariant features are observed, including
• the formation of small non coding RNAs like small interfering RNA (siRNA), microRNA (miRNA) from
the dsRNA that initiates the process
• The systemic transmission and amplification of the silencing signal from its site of initiation.
7. si RNA AND mi RNA
• si RNA, mi RNA are non-coding RNAs that are associated with RNA interference
• si RNA (or short/small interfering RNA) are produced either from exogenous (provided from the
outside) ds RNA introduced into the cell in the form of synthetic constructs/viral DNA. It can also be
generated endogenously
• mi RNA (micro RNA) are always produced from endogenous gene products (coded by the genome)
• As much as 5% of the human genome is dedicated to encoding and producing the >1,000 miRNAs that
regulate at least 30% of our genes
•
8. DICER
• Dicer is the enzyme that cleaves dsRNA into siRNA
• It belongs to the rnase III nuclease family
• Rnase III family members are among the few nucleases that show specificity for dsRNAs
• Dicer has four distinct domains:
• An amino-terminal helicase domain,
• Dual RNAse III motifs,
• A dsRNA binding domain, and
• A PAZ domain (a 110-amino-acid domain present in proteins like piwi, argo, and zwille/pinhead)
• Cleavage by dicer is thought to be catalyzed by its tandem rnase III domains.
9. RNA INDUCED SILENCING COMPLEX(RISC)
• Is a multicomponent protein complex
• One of the protein components of this complex was identified as a member of the argonaute family of
proteins and was termed argonaute2 (AGO2)
• AGO2 is a 130-kda protein containing polyglutamine residues, PAZ, and PIWI domains characteristic of
members of the argonaute gene family
• AGO2 bears catalytic activity and can cleave the target mRNA
• RISC also contains other proteins including RNA binding proteins, helicase proteins etc
• A few molecules of dsRNA are sufficient to degrade a continuously transcribed target mRNA for a
long period of time.
10. siRNA MEDIATED RNA-I
Initiation:
• processing of dsRNA into siRNAs
• Input dsRNA introduced directly or via a transgene or virus is digested into 21-23 nucleotide small
interfering RNAs (siRNAs)
• siRNAs are formed and accumulate as double-stranded RNA molecules of defined chemical
structures
• Each strand of siRNA has 5-phosphate and 3-hydroxyl termini and 2- to 3-nucleotide 3 overhangs.
• SiRNAs are produced when the enzyme dicer, a member of the RNase iii family of dsRNA-specific
ribonucleases, cleaves dsRNA in an atp-dependent manner
11. Effector step:
• The si RNA is then loaded on to a protein complex called as RNA induced silencing complex(RISC).
• The loading is assisted by the risc-loading complex (RLC) comprised of the DICER and dsRNA-binding
protein
• Inside the RISC the siRNA unwinds in an ATP dependant activity.
• One of the strands is called the guide strand (the strand complementary to the cognate mRNA) and the
other is called the passenger strand.
• The passenger strand is discarded
• The guide strand remains associated with the argonaut protein of the RISC
• The guide strand targets the RISC to the cognate mRNA and the RISC proteins through diverse
mechanisms prevent the mRNA from being translated