The document describes a study that investigated the effects of an enriched environment on rat behavior and response to pharmacological interventions. Rats were housed in either a standard environment or an enriched one involving more space, objects, and stimulation. They underwent tests for anxiety, learning, and memory, including an open field test, Morris water maze, and object recognition task. Results showed enriched rats had less anxiety-like behavior, better spatial learning and memory, and a stronger preference for novel objects after a delay. However, housing had little effect on response to the cognitive impairing drug scopolamine. The study suggests an enriched environment can improve rat behavior but may not alter response to all drugs.
Pathogenesis-related proteins (initially named “b” proteins) were discovered in tobacco leaves
hypersensitively reacting to TMV by two independently working groups (Van Loon and Van Kammen,
1970; Gianinazzi et al., 1970)
Gene stacking and its materiality in crop improvementShamlyGupta
Gene stacking involves combining two or more transgenes into a host plant genome. It can be achieved through iterative crossing of transgenic plants, re-transformation of transgenic plants with additional genes, or co-transformation of multiple genes simultaneously. Co-transformation allows multiple genes to be introduced together but risks silencing effects if the same promoter is used. Iterative crossing is time-consuming but avoids this issue. Gene stacking holds promise for improving crop traits like disease resistance and nutrition but careful selection is needed to maintain expression levels of all genes. Recent examples demonstrate progress in stacking drought tolerance, yield, and nutrition genes into elite crop varieties.
Chitinase genes and insect management in crop plantsSenthil Natesan
The document discusses chitin genes and insect management in crop plants. It provides details on the structure and location of chitin in insects. It describes the pathways and enzymes involved in chitin synthesis and degradation. It discusses the classification, characteristics, and molecular structure of chitinase enzymes from insects, fungi, plants and bacteria. It summarizes approaches to overexpress chitinase genes in transgenic plants and fungi for insect pest management.
The document discusses the CRISPR/Cas9 system. It describes how CRISPR/Cas9 uses a Cas9 protein guided by a single guide RNA to recognize and cut target DNA. The system has three stages: adaptation, expression and processing of CRISPR RNA, and interference where the Cas9 protein complex cuts the target DNA. CRISPR/Cas9 can be engineered to act as a nuclease, nickase, or inactive dead Cas9 for gene regulation applications like activation or repression. It provides a gift from nature for precise genome editing and regulation.
CRISPR is a new gene-editing tool that has significant promise but also requires regulation. It allows for precise editing of DNA by using guide RNA and an enzyme called Cas9. This advance enables basic scientists to create transgenic animal models, agricultural scientists to develop disease-resistant crops, and medical scientists to potentially cure and prevent genetic diseases. However, it also raises concerns about potential misuse by the military, wealthy individuals, or rogue scientists. As a result, CRISPR will be one of the biggest scientific issues of the next decade, and responsible innovation organizations should determine their stance, talk to researchers, work with governing bodies like NAS, and help convey both benefits and needed oversight of this technology.
This document discusses the shifted multiplicative model (SHMM) for analyzing genotype-by-environment interactions. The SHMM allows for the separation of genotypic and environmental effects as well as the identification of crossover and non-crossover interactions. The document provides an example of using the SHMM to cluster 41 wheat genotypes tested across 7 environments into 9 clusters with insignificant crossover interactions. It demonstrates how the SHMM can help breeders group similar environments and select superior genotypes for different conditions.
This document provides an overview of genome engineering techniques from older methods to newer CRISPR/Cas9 technology. It discusses how genes can be transferred between organisms using vectors like plasmids or viruses. Older techniques like ZFN and TALEN cut DNA at specific sites, while CRISPR/Cas9 uses a Cas9 enzyme guided by CRISPR RNA to make precise cuts. Delivery methods for Cas9 include plasmids, mRNA, and RNP complexes. Viral vectors like AAV are commonly used but have limits. Physical methods also deliver Cas9 via nanoparticles or peptides.
Pathogenesis-related proteins (initially named “b” proteins) were discovered in tobacco leaves
hypersensitively reacting to TMV by two independently working groups (Van Loon and Van Kammen,
1970; Gianinazzi et al., 1970)
Gene stacking and its materiality in crop improvementShamlyGupta
Gene stacking involves combining two or more transgenes into a host plant genome. It can be achieved through iterative crossing of transgenic plants, re-transformation of transgenic plants with additional genes, or co-transformation of multiple genes simultaneously. Co-transformation allows multiple genes to be introduced together but risks silencing effects if the same promoter is used. Iterative crossing is time-consuming but avoids this issue. Gene stacking holds promise for improving crop traits like disease resistance and nutrition but careful selection is needed to maintain expression levels of all genes. Recent examples demonstrate progress in stacking drought tolerance, yield, and nutrition genes into elite crop varieties.
Chitinase genes and insect management in crop plantsSenthil Natesan
The document discusses chitin genes and insect management in crop plants. It provides details on the structure and location of chitin in insects. It describes the pathways and enzymes involved in chitin synthesis and degradation. It discusses the classification, characteristics, and molecular structure of chitinase enzymes from insects, fungi, plants and bacteria. It summarizes approaches to overexpress chitinase genes in transgenic plants and fungi for insect pest management.
The document discusses the CRISPR/Cas9 system. It describes how CRISPR/Cas9 uses a Cas9 protein guided by a single guide RNA to recognize and cut target DNA. The system has three stages: adaptation, expression and processing of CRISPR RNA, and interference where the Cas9 protein complex cuts the target DNA. CRISPR/Cas9 can be engineered to act as a nuclease, nickase, or inactive dead Cas9 for gene regulation applications like activation or repression. It provides a gift from nature for precise genome editing and regulation.
CRISPR is a new gene-editing tool that has significant promise but also requires regulation. It allows for precise editing of DNA by using guide RNA and an enzyme called Cas9. This advance enables basic scientists to create transgenic animal models, agricultural scientists to develop disease-resistant crops, and medical scientists to potentially cure and prevent genetic diseases. However, it also raises concerns about potential misuse by the military, wealthy individuals, or rogue scientists. As a result, CRISPR will be one of the biggest scientific issues of the next decade, and responsible innovation organizations should determine their stance, talk to researchers, work with governing bodies like NAS, and help convey both benefits and needed oversight of this technology.
This document discusses the shifted multiplicative model (SHMM) for analyzing genotype-by-environment interactions. The SHMM allows for the separation of genotypic and environmental effects as well as the identification of crossover and non-crossover interactions. The document provides an example of using the SHMM to cluster 41 wheat genotypes tested across 7 environments into 9 clusters with insignificant crossover interactions. It demonstrates how the SHMM can help breeders group similar environments and select superior genotypes for different conditions.
This document provides an overview of genome engineering techniques from older methods to newer CRISPR/Cas9 technology. It discusses how genes can be transferred between organisms using vectors like plasmids or viruses. Older techniques like ZFN and TALEN cut DNA at specific sites, while CRISPR/Cas9 uses a Cas9 enzyme guided by CRISPR RNA to make precise cuts. Delivery methods for Cas9 include plasmids, mRNA, and RNP complexes. Viral vectors like AAV are commonly used but have limits. Physical methods also deliver Cas9 via nanoparticles or peptides.
CRISPR/Cas9 is a powerful new technique for genome editing that allows DNA to be easily cut and modified. It involves using the Cas9 enzyme, guided by RNA, to create targeted double-stranded breaks in DNA which are then repaired, allowing the DNA sequence to be altered. This system was adapted from a bacterial immune system. CRISPR/Cas9 represents a major breakthrough as it is simpler, cheaper and more accurate than previous genome editing methods. It has already been used to edit genes in numerous organisms and holds promise for applications like correcting genetic diseases. However, off-target effects and ethical concerns surrounding its use in humans remain limitations that need to be addressed.
An overview of agricultural applications of genome editing: Crop plantsOECD Environment
The presentation gives an overview of genome editing applications in relation to crop plants. The aim is to have a better understanding of the specific features of genome editing in comparison with classical breeding and genetic engineering techniques. It will give an overview of some examples of agricultural applications that may be on or close to the market or under research and development. It will also consider the possibility of foreseeing future applications (e.g. variations in CRISPR/Cas applications, DNA-free application, agricultural pest control), if possible.
This document provides an overview of designing CRISPR/Cas9 based genome editing in crop plants. It discusses selecting a target gene, constructing the CRISPR/Cas9 system using Cas9 protein and guide RNA, adding gene regulatory elements like promoters and terminators, designing constructs, transforming plants using various methods, and validating genome edits using techniques like sequencing, phenotyping, and molecular assays. The goal is to use this gene editing tool to introduce traits like disease resistance, drought tolerance, and improved nutrition in crop plants.
Metabolic engineering for oil quality improvementSenthil Natesan
The most important oilseed crops are Oil palm, Soybeans, Rapeseed and Sunflower,which together account for ≈ 79% of the total production of oils.Oils that are low in palmitic acid and rich in either oleic acid or stearic acid are novel oils. Selective breeding utilizing natural variants or induced mutations has been used to develop a range of improved oils. The vegetable oil is used for different applications as renewable sources of food used for frying, baking, processed foods,Fuel (Biodiesel),medicine and can be used as industrial raw material for preparation of soaps, detergents, paints, lubricants etc.
The recommended ratio of omega6/omega3 fatty acids in the human diet is approximately 2:1 to 6:1 (Simopoulos., 2000; Wijendran and Hayes., 2004) and the much higher ratio of omega 6 fatty acids in the typical Western diet (approximately 20:1) is thought to be a major contributor to cardiovascular disease (Simopoulos., 2000).
For metabolic engineering of oil quality improvement fatty acid composition and enzymes involved are very important so we can reduce expression of endogenous enzymes by adding new enzyme ,overexpressing existing enzyme and by using antisense RNA. It proved that genes for membrane-bound fatty acid-modifying enzymes not only from plants but also from bacterial,animal,yeast have been shown to function in transgenic plants.The enzymes such as Fatty acid synthase ,Thioesterases ,Elongases ,Desaturases ,Stearoyl-ACP desaturase ,Δ12-desaturase, , Δ15-Desaturase ,Acyltransferases and Hydroxylases are important in fatty acid manipulation.Suppression of the oleate D12-desaturase gene (which normally converts 18:1 to 18:2) in soybean, sunflower, cotton and canola has resulted in the production of oils with a high oleic acid content, which have greater oxidative stability and improved performance in high-temperature cooking applications. (Metzger and Bornscheuer., 2006).
Plant disease resistance occurs through both pre-formed structures and infection-induced immune responses. There are two tiers of the plant immune system - pattern-triggered immunity (PTI) triggered by pathogen-associated molecular patterns (PAMPs), and effector-triggered immunity (ETI) triggered by recognition of pathogen effectors through resistance (R) proteins. Quantitative resistance involving multiple genes provides more durable resistance than major gene resistance. Genetic engineering and breeding can enhance crop disease resistance through introduction of R genes or resistance mechanisms.
This document discusses the application of genomics in improving crop plants. It explains that genomics tools like tissue culture, genetic engineering, molecular diagnostics and molecular markers have revolutionized crop breeding programs. Specifically, it describes how tissue culture allows for rapid propagation of disease-free plants at scale. It also outlines how genetic engineering has been used to develop transgenic crops with improved traits like herbicide tolerance, pathogen resistance, stress tolerance, fruit quality and pest resistance. Molecular diagnostics using probes and monoclonal antibodies enable early disease detection. Molecular markers aid in selecting desirable traits at early stages.
CRISPR-Cas is a natural defense system in bacteria that uses CRISPR sequences and Cas proteins to target and degrade foreign DNA such as from viruses. It has been adapted for genome editing in other organisms using a Cas9 protein guided by a synthetic single guide RNA to introduce targeted double-strand breaks. This system allows for precise genome modifications and has applications in biomedical research, disease treatment, and engineering of plants and other organisms. However, off-target effects and delivery methods require further optimization.
Restriction endonucleases are enzymes produced by bacteria that recognize specific sequences in foreign DNA and cut the DNA at or near the recognition sites. They function as part of the bacterial immune system to degrade foreign DNA. Restriction endonucleases cut DNA into fragments that have either blunt or sticky ends, depending on where they cut the DNA strands. They are named based on the bacteria that produces them and are classified into three types depending on their cleavage patterns. Type II restriction endonucleases cut directly at their recognition sites and produce fragments with sticky or blunt ends, making them useful for genetic engineering applications.
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.
This document contains a 40 question multiple choice exam on molecular biology. The exam covers topics such as DNA and RNA structure, gene expression, DNA replication, transcription, translation, gene regulation, and techniques used in molecular biology like PCR, DNA cloning, hybridization probes, and restriction enzymes. The second section asks students to answer 4 out of 5 long answer questions covering topics like ribosomes, cDNA libraries, gene cloning steps, hybridization probes, and polymerase chain reaction.
Thousands of different long non-coding RNAs (lncRNAs) exist in mammalian cells. lncRNAs do not encode proteins but can be very important for cell function. Studying their functions can be difficult because of their diverse modes of action. One method to discern cellular function is by selective knockdown of a specific lncRNA species. However, achieving consistent knockdown has proven to be more challenging for lncRNAs than for mRNAs or miRNAs. In this presentation, we discuss some of the issues encountered with lncRNA research. We cover antisense oligonucleotide (ASO) and small interfering RNA (siRNA) methods for lncRNA knockdown. And, we show how cellular localization of a specific lncRNA target informs the choice of knockdown method.
This document provides information on CRISPR Cas9 genome editing. It discusses the history and discovery of CRISPR dating back to 1987. It describes the key components of the CRISPR Cas9 system including Cas9 proteins, CRISPR RNA, protospacers, and PAM sequences. The mechanisms of how CRISPR Cas9 edits genomes through double strand breaks is explained. Finally, applications of CRISPR Cas9 are summarized, including using it to correct genetic mutations causing diseases in animals and potential applications in humans.
Yeast two hybrid system / protein-protein interactionMaryam Shakeel
The document discusses the yeast two-hybrid system, which is a technique used to detect protein-protein interactions in vivo. It involves fusing a bait protein to a DNA-binding domain and a prey protein to an activating domain; if the bait and prey proteins interact, they bring the domains together and activate transcription of a reporter gene. This allows researchers to efficiently study protein interactions, characterize the domains involved, and identify conditions required for interaction. However, the yeast two-hybrid system is limited to proteins that can localize and function properly in the yeast cell.
The document discusses loop-mediated isothermal amplification (LAMP) as a simple, rapid diagnostic tool for detecting microbial diseases. LAMP can amplify DNA under isothermal conditions in less than an hour using a single-tube reaction. It uses a set of six special primers that recognize eight distinct sequences on the target DNA to achieve high specificity. By utilizing a polymerase with strand displacement activity, LAMP amplifies DNA without the need for thermal cycling, producing large amounts of target DNA. This allows for visual detection of results without gel electrophoresis.
This document provides an overview of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and its role as an adaptive immune system in prokaryotes. It describes the components and function of the CRISPR-Cas system, including how it provides immunity against viruses and plasmids. Applications of CRISPR technology discussed include phage resistance in bacteria, gene regulation, and bacterial strain typing. Potential future uses involve harnessing CRISPR biology for applications like transcriptional control.
The document discusses gene regulatory networks (GRNs), including what they are, how they work, methods for modeling and analyzing them, and future challenges. Specifically, it notes that GRNs are networks of genes, proteins, and molecules that interact to control gene transcription. They respond to environmental signals and regulate processes like development. Computational models are needed to understand their complex behaviors under different conditions. Examples of models discussed include Boolean networks that represent gene expression levels as binary on/off states, continuous models that capture a range of expression levels, and stochastic models that account for random reactions.
Degradome sequencing and small RNA targetsMuhammed Ameer
small RNAs are Short (~18-30 nucleotides) Non-coding molecules.
Elucidation of miRNA function depends on the recognition of their target molecules (mRNA transcripts)
RNA degradation is a constant reaction in the living cells
The total products from RNA decay are uniformly defined as RNA degradome
Degradome sequencing is a powerful technique for the detection of cleavage sites of miRNA targets
Connects high-throughput Next-Generation Sequencing (NGS) and target predictions for miRNAs
Degradome sequencing can provide information about transcripts that undergo degradation by miRNAs
3 case studies
Muhammed Ameer
Masters Seminar - 2022
Department of Plant Biotechnology
Kerala Agricultural University
Use of CRISPR-Cas9 has revolutionized targeted genome editing. However, rapid design of high-quality guide RNA (gRNA) sequences with high on-target and low off-target editing remains challenging. We implemented a machine learning algorithm to design high-quality gRNA sequences in 5 commonly used species (human, mouse, rat, zebrafish, and nematode). Our tool also designs gRNA sequences against custom targets, and can check existing gRNA designs for quality. In this webinar, we review our data illustrating this tool's performance and demonstrate its use in predicting and designing improved gRNAs for genome editing.
El documento describe la historia y naturaleza del CrossFit. Fue creado en 1974 por Greg Glassman para enfocarse en un programa de entrenamiento de alta intensidad que incluye variados movimientos funcionales. El CrossFit consiste en ejercicios constantes y funcionales realizados a alta intensidad para desarrollar fuerza, tono muscular y funcionalidad. También se describe cómo el CrossFit se ha convertido en un estilo de vida que promueve buena alimentación y comunidad.
CRISPR/Cas9 is a powerful new technique for genome editing that allows DNA to be easily cut and modified. It involves using the Cas9 enzyme, guided by RNA, to create targeted double-stranded breaks in DNA which are then repaired, allowing the DNA sequence to be altered. This system was adapted from a bacterial immune system. CRISPR/Cas9 represents a major breakthrough as it is simpler, cheaper and more accurate than previous genome editing methods. It has already been used to edit genes in numerous organisms and holds promise for applications like correcting genetic diseases. However, off-target effects and ethical concerns surrounding its use in humans remain limitations that need to be addressed.
An overview of agricultural applications of genome editing: Crop plantsOECD Environment
The presentation gives an overview of genome editing applications in relation to crop plants. The aim is to have a better understanding of the specific features of genome editing in comparison with classical breeding and genetic engineering techniques. It will give an overview of some examples of agricultural applications that may be on or close to the market or under research and development. It will also consider the possibility of foreseeing future applications (e.g. variations in CRISPR/Cas applications, DNA-free application, agricultural pest control), if possible.
This document provides an overview of designing CRISPR/Cas9 based genome editing in crop plants. It discusses selecting a target gene, constructing the CRISPR/Cas9 system using Cas9 protein and guide RNA, adding gene regulatory elements like promoters and terminators, designing constructs, transforming plants using various methods, and validating genome edits using techniques like sequencing, phenotyping, and molecular assays. The goal is to use this gene editing tool to introduce traits like disease resistance, drought tolerance, and improved nutrition in crop plants.
Metabolic engineering for oil quality improvementSenthil Natesan
The most important oilseed crops are Oil palm, Soybeans, Rapeseed and Sunflower,which together account for ≈ 79% of the total production of oils.Oils that are low in palmitic acid and rich in either oleic acid or stearic acid are novel oils. Selective breeding utilizing natural variants or induced mutations has been used to develop a range of improved oils. The vegetable oil is used for different applications as renewable sources of food used for frying, baking, processed foods,Fuel (Biodiesel),medicine and can be used as industrial raw material for preparation of soaps, detergents, paints, lubricants etc.
The recommended ratio of omega6/omega3 fatty acids in the human diet is approximately 2:1 to 6:1 (Simopoulos., 2000; Wijendran and Hayes., 2004) and the much higher ratio of omega 6 fatty acids in the typical Western diet (approximately 20:1) is thought to be a major contributor to cardiovascular disease (Simopoulos., 2000).
For metabolic engineering of oil quality improvement fatty acid composition and enzymes involved are very important so we can reduce expression of endogenous enzymes by adding new enzyme ,overexpressing existing enzyme and by using antisense RNA. It proved that genes for membrane-bound fatty acid-modifying enzymes not only from plants but also from bacterial,animal,yeast have been shown to function in transgenic plants.The enzymes such as Fatty acid synthase ,Thioesterases ,Elongases ,Desaturases ,Stearoyl-ACP desaturase ,Δ12-desaturase, , Δ15-Desaturase ,Acyltransferases and Hydroxylases are important in fatty acid manipulation.Suppression of the oleate D12-desaturase gene (which normally converts 18:1 to 18:2) in soybean, sunflower, cotton and canola has resulted in the production of oils with a high oleic acid content, which have greater oxidative stability and improved performance in high-temperature cooking applications. (Metzger and Bornscheuer., 2006).
Plant disease resistance occurs through both pre-formed structures and infection-induced immune responses. There are two tiers of the plant immune system - pattern-triggered immunity (PTI) triggered by pathogen-associated molecular patterns (PAMPs), and effector-triggered immunity (ETI) triggered by recognition of pathogen effectors through resistance (R) proteins. Quantitative resistance involving multiple genes provides more durable resistance than major gene resistance. Genetic engineering and breeding can enhance crop disease resistance through introduction of R genes or resistance mechanisms.
This document discusses the application of genomics in improving crop plants. It explains that genomics tools like tissue culture, genetic engineering, molecular diagnostics and molecular markers have revolutionized crop breeding programs. Specifically, it describes how tissue culture allows for rapid propagation of disease-free plants at scale. It also outlines how genetic engineering has been used to develop transgenic crops with improved traits like herbicide tolerance, pathogen resistance, stress tolerance, fruit quality and pest resistance. Molecular diagnostics using probes and monoclonal antibodies enable early disease detection. Molecular markers aid in selecting desirable traits at early stages.
CRISPR-Cas is a natural defense system in bacteria that uses CRISPR sequences and Cas proteins to target and degrade foreign DNA such as from viruses. It has been adapted for genome editing in other organisms using a Cas9 protein guided by a synthetic single guide RNA to introduce targeted double-strand breaks. This system allows for precise genome modifications and has applications in biomedical research, disease treatment, and engineering of plants and other organisms. However, off-target effects and delivery methods require further optimization.
Restriction endonucleases are enzymes produced by bacteria that recognize specific sequences in foreign DNA and cut the DNA at or near the recognition sites. They function as part of the bacterial immune system to degrade foreign DNA. Restriction endonucleases cut DNA into fragments that have either blunt or sticky ends, depending on where they cut the DNA strands. They are named based on the bacteria that produces them and are classified into three types depending on their cleavage patterns. Type II restriction endonucleases cut directly at their recognition sites and produce fragments with sticky or blunt ends, making them useful for genetic engineering applications.
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.
This document contains a 40 question multiple choice exam on molecular biology. The exam covers topics such as DNA and RNA structure, gene expression, DNA replication, transcription, translation, gene regulation, and techniques used in molecular biology like PCR, DNA cloning, hybridization probes, and restriction enzymes. The second section asks students to answer 4 out of 5 long answer questions covering topics like ribosomes, cDNA libraries, gene cloning steps, hybridization probes, and polymerase chain reaction.
Thousands of different long non-coding RNAs (lncRNAs) exist in mammalian cells. lncRNAs do not encode proteins but can be very important for cell function. Studying their functions can be difficult because of their diverse modes of action. One method to discern cellular function is by selective knockdown of a specific lncRNA species. However, achieving consistent knockdown has proven to be more challenging for lncRNAs than for mRNAs or miRNAs. In this presentation, we discuss some of the issues encountered with lncRNA research. We cover antisense oligonucleotide (ASO) and small interfering RNA (siRNA) methods for lncRNA knockdown. And, we show how cellular localization of a specific lncRNA target informs the choice of knockdown method.
This document provides information on CRISPR Cas9 genome editing. It discusses the history and discovery of CRISPR dating back to 1987. It describes the key components of the CRISPR Cas9 system including Cas9 proteins, CRISPR RNA, protospacers, and PAM sequences. The mechanisms of how CRISPR Cas9 edits genomes through double strand breaks is explained. Finally, applications of CRISPR Cas9 are summarized, including using it to correct genetic mutations causing diseases in animals and potential applications in humans.
Yeast two hybrid system / protein-protein interactionMaryam Shakeel
The document discusses the yeast two-hybrid system, which is a technique used to detect protein-protein interactions in vivo. It involves fusing a bait protein to a DNA-binding domain and a prey protein to an activating domain; if the bait and prey proteins interact, they bring the domains together and activate transcription of a reporter gene. This allows researchers to efficiently study protein interactions, characterize the domains involved, and identify conditions required for interaction. However, the yeast two-hybrid system is limited to proteins that can localize and function properly in the yeast cell.
The document discusses loop-mediated isothermal amplification (LAMP) as a simple, rapid diagnostic tool for detecting microbial diseases. LAMP can amplify DNA under isothermal conditions in less than an hour using a single-tube reaction. It uses a set of six special primers that recognize eight distinct sequences on the target DNA to achieve high specificity. By utilizing a polymerase with strand displacement activity, LAMP amplifies DNA without the need for thermal cycling, producing large amounts of target DNA. This allows for visual detection of results without gel electrophoresis.
This document provides an overview of CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) and its role as an adaptive immune system in prokaryotes. It describes the components and function of the CRISPR-Cas system, including how it provides immunity against viruses and plasmids. Applications of CRISPR technology discussed include phage resistance in bacteria, gene regulation, and bacterial strain typing. Potential future uses involve harnessing CRISPR biology for applications like transcriptional control.
The document discusses gene regulatory networks (GRNs), including what they are, how they work, methods for modeling and analyzing them, and future challenges. Specifically, it notes that GRNs are networks of genes, proteins, and molecules that interact to control gene transcription. They respond to environmental signals and regulate processes like development. Computational models are needed to understand their complex behaviors under different conditions. Examples of models discussed include Boolean networks that represent gene expression levels as binary on/off states, continuous models that capture a range of expression levels, and stochastic models that account for random reactions.
Degradome sequencing and small RNA targetsMuhammed Ameer
small RNAs are Short (~18-30 nucleotides) Non-coding molecules.
Elucidation of miRNA function depends on the recognition of their target molecules (mRNA transcripts)
RNA degradation is a constant reaction in the living cells
The total products from RNA decay are uniformly defined as RNA degradome
Degradome sequencing is a powerful technique for the detection of cleavage sites of miRNA targets
Connects high-throughput Next-Generation Sequencing (NGS) and target predictions for miRNAs
Degradome sequencing can provide information about transcripts that undergo degradation by miRNAs
3 case studies
Muhammed Ameer
Masters Seminar - 2022
Department of Plant Biotechnology
Kerala Agricultural University
Use of CRISPR-Cas9 has revolutionized targeted genome editing. However, rapid design of high-quality guide RNA (gRNA) sequences with high on-target and low off-target editing remains challenging. We implemented a machine learning algorithm to design high-quality gRNA sequences in 5 commonly used species (human, mouse, rat, zebrafish, and nematode). Our tool also designs gRNA sequences against custom targets, and can check existing gRNA designs for quality. In this webinar, we review our data illustrating this tool's performance and demonstrate its use in predicting and designing improved gRNAs for genome editing.
El documento describe la historia y naturaleza del CrossFit. Fue creado en 1974 por Greg Glassman para enfocarse en un programa de entrenamiento de alta intensidad que incluye variados movimientos funcionales. El CrossFit consiste en ejercicios constantes y funcionales realizados a alta intensidad para desarrollar fuerza, tono muscular y funcionalidad. También se describe cómo el CrossFit se ha convertido en un estilo de vida que promueve buena alimentación y comunidad.
The document provides tips for presenting like a professional by focusing on designing the presentation around the audience's needs, engaging and connecting with the audience, and delivering the presentation in a clear, confident, and impactful manner through effective use of body language, pacing, questions, and other presentation techniques. It emphasizes understanding the audience, crafting a simple yet compelling message, practicing to improve delivery skills, and striving to have a meaningful impact rather than perfection.
The document provides tips for conducting business effectively in the United States. It notes some key cultural differences like a focus on facts over opinions, the importance of timeliness, and avoiding discussions of sex, politics or religion. It advises treating meetings as opportunities to think big and focus on benefits like savings, revenue and reduced risks. The overall message is that understanding cultural norms and differences can help non-Americans navigate business in the United States.
The document provides tips for presenting like a professional by focusing on designing the presentation around the audience's needs, engaging and connecting with the audience, and delivering the presentation in a clear, confident, and impactful manner through effective use of body language, pacing, questions, and other presentation techniques. The tips cover aspects like understanding the audience, establishing credibility, structuring the opening minutes, using visual aids, handling questions, and practicing delivery.
This document outlines different terrestrial and aquatic ecosystems and discusses how human activity affects the environment. It describes forest, mountain grasslands, deserts and steppes as terrestrial ecosystems and marine ecosystems such as sandy beaches, rocky shores and the open sea as well as freshwater ecosystems like rivers and lagoons as aquatic ecosystems. The document also explains how pollution, deforestation, desertification, and endangered species are effects of human activity on the environment.
Brain aging and plasticity and environmental enrichment!Sara Hassan
This document summarizes research on successful brain aging. It finds that aging does not necessarily mean cognitive decline, and lifestyle factors can promote healthy brain aging through plasticity. Environmental enrichment, caloric restriction, certain nutrients like omega-3 fatty acids, aerobic exercise, and stress reduction all increase neurotrophic factors like BDNF and reduce damage, helping maintain brain function and delaying neurodegenerative diseases. While aging involves some anatomical and functional changes, lifestyle interventions can support optimal cognitive functioning throughout life.
Many environmental problems are caused by human actions including pollution, deforestation, desertification, and habitat loss. Pollution is the accumulation of harmful substances in the air, water, and ground. Deforestation is the disappearance of forests from cutting down trees. Desertification is the transformation of landscapes into desert areas as the soil becomes dry and poor. Habitat loss occurs when natural areas are destroyed for housing and industry. Children can help address these issues by reducing garbage production, avoiding cutting down trees, and protecting natural areas.
The document defines environmental pollution and describes its three main types: air, water, and soil pollution. It provides details on the causes and effects of each type of pollution. Air pollution is caused by emissions from vehicles, factories, and burning of fossil fuels, and can lead to acid rain, haze, health issues, and depletion of the ozone layer. Water pollution results from industrial waste, oil spills, and waste disposal in rivers and oceans, harming wildlife and spreading disease. Soil pollution is caused by industrial chemicals, mining, pesticides, and landfills, contaminating groundwater and reducing soil fertility.
The 7 Key Components of a Perfect Elevator Pitch by @noahparsonsPalo Alto Software
Whether you are trying to raise money for your business or just want to perfect your business strategy, a solid elevator pitch is an essential tool for achieving your goals.
An elevator pitch can be delivered either verbally, ideally in 60 seconds or less, or as a one-page overview of your business.
Think of the elevator pitch as an executive summary that provides a quick overview of your business and details why you are going to be successful.
Biography and career history of Bruno AmezcuaBruno Amezcua
Bruno Amezcua's entry into the film and visual arts world seemed predestined. His grandfather, a distinguished film editor from the 1950s through the 1970s, profoundly influenced him. This familial mentorship early on exposed him to the nuances of film production and a broad array of fine arts, igniting a lifelong passion for narrative creation. Over 15 years, Bruno has engaged in diverse projects showcasing his dedication to the arts.
At Affordable Garage Door Repair, we specialize in both residential and commercial garage door services, ensuring your property is secure and your doors are running smoothly.
The Fascinating World of Bats: Unveiling the Secrets of the Nightthomasard1122
The Fascinating World of Bats: Unveiling the Secrets of the Night
Bats, the mysterious creatures of the night, have long been a source of fascination and fear for humans. With their eerie squeaks and fluttering wings, they have captured our imagination and sparked our curiosity. Yet, beyond the myths and legends, bats are fascinating creatures that play a vital role in our ecosystem.
There are over 1,300 species of bats, ranging from the tiny Kitti's hog-nosed bat to the majestic flying foxes. These winged mammals are found in almost every corner of the globe, from the scorching deserts to the lush rainforests. Their diversity is a testament to their adaptability and resilience.
Bats are insectivores, feeding on a vast array of insects, from mosquitoes to beetles. A single bat can consume up to 1,200 insects in an hour, making them a crucial part of our pest control system. By preying on insects that damage crops, bats save the agricultural industry billions of dollars each year.
But bats are not just useful; they are also fascinating creatures. Their ability to fly in complete darkness, using echolocation to navigate and hunt, is a remarkable feat of evolution. They are also social animals, living in colonies and communicating with each other through a complex system of calls and body language.
Despite their importance, bats face numerous threats, from habitat destruction to climate change. Many species are endangered, and conservation efforts are necessary to protect these magnificent creatures.
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4. Introduction
Rats frequently used as an animal model in
psychopharmacological research
How comparable are they? (Patterson-Kane, Hunt & Harper, 1999).
People: everyday novel objects
Standard rats: always same environment
Enriched rats (with novel objects) better?
5. Enriched environment?
Larger group of animals (Hamm, Temple, O’Dell, Pike &
Lyeth, 1996; Wainwright et al., 1993)
More room to move arround (Arai & Feig, 2010; Hamm et
al., 1996; Wainwright et al., 1993).
Lots of different object, stimulating all senses (Bennet et
al., 1964; Hamm et al., 1996)
6. Advantages enriched
environment
More dendritic arborisation, neurogenesis, glial cells and
improved learning (Kempermann, Kuhn, & Gage, 1997).
More synaptic plasticity (Rampon et al., 2000).
The best way to investigate these advantages is the
performance on different tasks (Cao, Huang, and Ruan,
2008).
Effect on pharmacological interventions?
7. Open Field test (Hall, 1934)
Measures anxiety and exploratory behaviour
(Wainwright et al., 1993).
The field is divided into different areas: wall, corner and
centre
Measures: behaviour and time spend in different areas
open field.
Anxiety: more time in corners and near wall, low distance
moved, more boli (Walsh & Cummins, 1976)
Exploratory behaviour: Number of rears and leans, and
high distance moved.
8. Morris water maze (Morris, 1981)
Measures spatial learning and memory (Morris, 1981)
Circular tank, filled with water, with a platform placed
beneath water surface (Buccafusco, 2009).
Rats will find the platform faster everyday regardless of
starting position.
Measures: Swimming speed, distance moved, time in the
zone of the platform.
Probe trials: no platform, check whether rats still know
the location of the platform.
9. Object Recognition task
AKA Novel object preference task (Mumby, Gaskin, Glenn,
Schramek & Lehmann, 2002)
Two trails: one trial with two similar objects and one trial
with an old and a new object (Mumby et al., 2002)
Rats have preference for novel object (Dix & Aggleton,
1998; Ennaceur & Delacour, 1988)
Looking at novel object correlates with memory of the
familiar objects (Ennaceur & Delacour, 1988)
10. Scopolamine
Cognitive impairing drug, blocks muscarinic receptors
Animal model of Alzheimer’s disease
How will the environment influence the effect of
scopolamine on memory?
Hypothesis: For enriched rats more scopolamine is
needed to achieve a memory impairing effect.
11.
12. Methods
36 Male Wistar
Rats
18 Standard 18 Enriched
condition Condition
13. From six weeks of age placed in
enviroment
Tests started with 12 weeks
Used to human contact
Reversed light-dark cycle: lights on from
19:00-7:00
Unlimited access to food and water
21 C 1 C, humidity 45%-55%
14. Standard
Three rats per cage six cages
40cm long x 20cm high x 25cm wide
Objects
Cardboard tube
Wooden stick
Sawdust bedding
16. Enriched
Two large cages with nine rats each
150cm long x 80cm high x 90cm wide
Environment changed and cleaned every week
Novel stimuli
Objects: PVC pipes, treadmills, brick stones, metal grid,
rope, wood sticks, different types of nesting material.
17. Tests we used:
Open field test
Anxiety behaviour
Morris water maze
Learning
Object Recognition task (novel object preference task)
Memory
18. Open field
Square box: 1m x 1m, grey floor
Tested four days in a row, day 4 had novel object
Five minutes exploration time
Measurements
By computer programme (EthoVision)
Distance moved, time near walls, time in centre, time in
corner
By human
Rears, leans, boli
19. Morris water maze
Large water tank: 122cm ø, 80cm height
Small platform placed 40cm from wall and 1cm below
water surface
Four different starting positions
Acquistion trial: 4 days in a row, 4 trials/day
Probe trial: day 3 (trial nr 5) and day 5 (trial nr 1)
Reversal trials (other platform location): day 5 and 6, 4
trials/day
EthoVision is used for the measurements
20. Object Recognition task
Rats placed in round box, 1 transparent side
3 minutes exploration time each trial
Trial1: two similar objects
Trial2: one familiar object (like in trial1) and one new object.
Mug, jar, small bottle, cone
No medication
One hour delay
Twenty-four hour delay
With medication
One hour delay cognitive impairing drugs
27. Rears
There was only a group
effect between leaning
and distance travelled.
The standard rats had a
higher distance moved
and number of leans.
28. Analysis of the open-field (day 4)
Independent Measure Group Standard Enriched
variable
Distance travelled Anxiety/exploratory t= 5.03, df= 34, p < M= 1675.41, SD= M= 1218.90, SD=
behaviour .01 156.86, N=18 351.74, N= 18
Time in centre of Anxiety t= 2.12, df= 34, p < M= 50.60, SD= 13.07, M= 35.44, SD= 27.32,
field .05 N= 18 N= 18
Time in corners Anxiety n.s. M= 31.98, SD= 7.71, M= 54.51, SD= 26.19,
N=18 N= 18
Thigmotaxis/Time at Anxiety n.s. M= 60.81, SD= 10.37, M= 54.07, SD= 17.59,
wall N=18 N=18
Time spent at novel Exploratory n.s. M=6.61, SD= 5.45, N= M= 5.98, SD= 5.73,
object behaviour 18 N=18
Leaning Exploratory n.s. M= 19.42, SD= 5.72, M= 16.94, SD= 4.35,
behaviour N=18 N= 18
Rearing Exploratory n.s. M= 14.49, SD= 6.87, M= 16.37, SD= 5.71,
behaviour N= 18 N= 18
Boli Anxiety n.s. M= 3.61, SD= 3.26, M= 2.28, SD= 2.80,
N= 18 N= 18
29. Distance Moved
There was only a group
effect in the distance
moved and time spend in
centre. The standard rats
had again a higher
distance moved, and they
Time in Centre have spend more time in
the centre of the open
field.
30. Morris water maze
Acquisition trial
Acquisition trial Morris water maze (MWM)
Independent Measure Day Group Interaction
variable
Distance moved F(5,102) = 98.189, F(1,34) = 5.036, n.s.
p<0.001 p=0.031
Escape latency Learning F(3,102) = 78.374, n.s. n.s.
p<0.001
Mean velocity F(5,102) =7.868, n.s. n.s.
p<0.001
36. Object recognition task
No medication: • Effect of delay:
F(1,33) =24.348, P<0.001
• Group effect:
F(1, 33) = 5.133, P<0.05
D2 value is time spend at novel
object minus the time spend at No effects on total
old object corrected for exploration time or
exploration time preference for the left
or right object
37. Scopolamine
D2 Value
No effect on group:
F (1, 99) = 0.189, p=0.665
Dose effect:
F (2, 99) = 13.961, p<0.01
38. Exploration time trial1 (E1):
Group (n.s.):
F(1,98)= 1.720, p=0.193
Dose effect:
F(2,98)=3.111, p=0.049
Exploration time trial2 (E2):
Group (n.s.):
F(1,99) = 1.715. p=0.193
Dose:
F(2,99)= 6.602, p=0.002
39. Conclusions
Open field:
• Standard rats moved more on all four days
• Enriched rats spent more time in corners of open
field
• Leans and rears increase over time
• Number of defeciations decline
40. Morris water maze:
• Standard rats moved more
• Decline in distance moved over the days on both
groups
• Enriched rats spent more time in the west zone and
the zone of the platform during probe trials
41. Novel object preference task:
• Enriched rats have a stronger preference for the
novel object after 24 hours delay (no medication)
• With scopolamine there was a strong effect of the
dose, but no effect between groups on the
exploration time and the preference for the novel
object.
42.
43. Open field results: Habituation the key?
Crusio and Schwegler (1987) and Crusio (2001)
negatively correlate increased intra and infra
hippocampal mossy fibre (IIHMF) projections with
exploration.
Denenberg (1969) carried out a factor analysis of open
field behaviour and found that increased ambulation
was linked to anxious behaviour on only the first day.
Indicative of the opposite for subsequent days.
44. Problems with this interpretation...
1. Some of these experiments conducted on mice...
Wishaw and Tomie (1996) claim that rats and mice
are comparable for a range of behavioural tests (as
long as they don't involve water!). Neurobiological
differences may exist though...
2. Meshi et al. (2006) demonstrated that behavioural
differences caused by EE were not due to
neurogenesis observed in van Praag's experiments.
45. The importance of exercise for
enrichment
(a,f) = controls
(b,g) = learner
(c,h) = swimmer
(d,i) = runner
(e,j) = enrichment
In this experiment, enrichment
had no effect on proliferation,
but exercise did.
Enrichment did affect the
survival of the newborn cells
positively (85% vs. 56%).
46. Types of enrichment and standard conditions (Simpson & Kelly,
2011).
Social or physical
enrichment? Both?
Dissociable effects?
Standard housing conditions of
our rats did feature some physical
enrichment (stick, cardboard
tubes) along with moderate social
enrichment (two litter-mates).
Different combinations in the literature
47. Perhaps standard rats were too enriched...
Lots of research in the literature features singly housed rats
as controls. This deprivation state not a suitable control.
However, our results were not entirely anomalous. MWM
performance reflected previous research in that enriched
housing led to faster acquisition and more time spent in PZ
during probe trial.
48. Performance in the ORT
No significant difference was observed between STD and EE rats
in d2. There was a significant effect for dose at the lower dose,
however.
Has scopolamine outlived its usefulness? Klinkenberg and
Blokland (2010) affirm that scopolamine is an effective amnestic
drug. However, dissociating its peripheral from its CNS effects can
be challenging.
Any difference we would hope to observe between groups would
have to be mediated through central nervous effects. But
peripheral effects would not cause distinct differences in
discrimination between groups.