The document discusses challenges in developing crop varieties that are tolerant to abiotic stress such as heat and drought. It notes that while genome sequencing technology has advanced rapidly, allowing for cheaper and faster sequencing, phenotyping crops under stress conditions remains complex, time-consuming and resource-intensive. Initiatives at the International Center for Tropical Agriculture aim to establish phenotyping platforms to facilitate high-throughput field and controlled environment phenotyping using automated, non-invasive tools to help characterize plant responses and link genotypes to drought and heat tolerance traits.
An overview of agricultural applications of genome editing: Farm animals OECD Environment
The presentation will give an overview of genome editing applications in relation to farm animals. 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.
Farm animals in aquatic systems - Anna Troedsson-WargeliusOECD Environment
This document summarizes the application of genome editing techniques like CRISPR-Cas9 in farmed fish species. It discusses how the technology has been established in Atlantic salmon and other aquaculture species. Some potential applications mentioned include genetic containment of escaped farmed fish, improving filet quality, disease resistance, and moving traits between strains. Challenges in salmon farming around environmental impacts, disease, and sustainability are also summarized. Specific projects on making sterile salmon and altering omega-3 metabolism are highlighted. Responsible research practices and acknowledgements are included at the end.
Sleep and the Gut Microbiome-bioRxiv-199075 1Jon Lendrum
This document provides supplemental information on the methods used to administer antibiotics to deplete the gut microbiota, construct 16S metagenomic libraries from fecal samples, and analyze the resulting sequencing data. It describes how: (1) the initial antibiotic cocktail was too toxic and had to be modified by removing an antifungal and decreasing antibiotic concentrations, (2) 16S rRNA gene V3/V4 regions were amplified and sequenced, (3) sequencing reads were processed and clustered into OTUs using QIIME, and (4) alpha and beta diversity analyses were performed to characterize microbial communities. References are also provided.
This document summarizes research on genome editing in poultry. It discusses how gene editing could help address issues like disease resilience and food allergies in chickens. The researchers have used CRISPR-Cas9 to successfully edit genes in chicken primordial germ cells (PGCs) through direct injection. This led to heterozygous and homozygous gene deletions being passed down to subsequent generations. Applications mentioned include deleting allergenic proteins from eggs and improving resistance to avian influenza. The document acknowledges the team conducting this research and expresses hope that their work can enhance sustainability, health, and efficiency in poultry production while improving food safety.
Gene editing with CRISPR/Cas9: sorghum as a case studyapaari
This document summarizes a presentation on using CRISPR/Cas9 gene editing to improve sorghum. The presentation discusses using gene editing to increase grain size and protein content in sorghum, which could improve its use for animal feed. It describes ongoing research knocking out specific genes to increase grain size by over 10% and protein content by up to 24%. If successful, this could increase sorghum yields and protein per hectare for uses like poultry feed. The presentation notes that gene edited crops may not be classified as GMOs, depending on regulatory decisions, and outlines ongoing research using this technology in sorghum.
Base editing is being used to induce precise mutations in rice in order to accelerate crop improvement. Researchers developed a base editing-mediated gene evolution method to diversify the sequence of the rice acetolactate synthase 1 (OsALS1) gene, which codes for the target of herbicide resistance. Multiple sgRNAs were used to introduce mutations across the OsALS1 locus. Novel mutations were identified that conferred resistance to the herbicide bispyribac-sodium. The resistant mutation was then introduced into an elite rice cultivar through base editing to generate a new herbicide tolerant variety. This demonstrates how base editing can be used to artificially evolve genes and introduce beneficial traits into commercial crops.
The document discusses challenges in developing crop varieties that are tolerant to abiotic stress such as heat and drought. It notes that while genome sequencing technology has advanced rapidly, allowing for cheaper and faster sequencing, phenotyping crops under stress conditions remains complex, time-consuming and resource-intensive. Initiatives at the International Center for Tropical Agriculture aim to establish phenotyping platforms to facilitate high-throughput field and controlled environment phenotyping using automated, non-invasive tools to help characterize plant responses and link genotypes to drought and heat tolerance traits.
An overview of agricultural applications of genome editing: Farm animals OECD Environment
The presentation will give an overview of genome editing applications in relation to farm animals. 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.
Farm animals in aquatic systems - Anna Troedsson-WargeliusOECD Environment
This document summarizes the application of genome editing techniques like CRISPR-Cas9 in farmed fish species. It discusses how the technology has been established in Atlantic salmon and other aquaculture species. Some potential applications mentioned include genetic containment of escaped farmed fish, improving filet quality, disease resistance, and moving traits between strains. Challenges in salmon farming around environmental impacts, disease, and sustainability are also summarized. Specific projects on making sterile salmon and altering omega-3 metabolism are highlighted. Responsible research practices and acknowledgements are included at the end.
Sleep and the Gut Microbiome-bioRxiv-199075 1Jon Lendrum
This document provides supplemental information on the methods used to administer antibiotics to deplete the gut microbiota, construct 16S metagenomic libraries from fecal samples, and analyze the resulting sequencing data. It describes how: (1) the initial antibiotic cocktail was too toxic and had to be modified by removing an antifungal and decreasing antibiotic concentrations, (2) 16S rRNA gene V3/V4 regions were amplified and sequenced, (3) sequencing reads were processed and clustered into OTUs using QIIME, and (4) alpha and beta diversity analyses were performed to characterize microbial communities. References are also provided.
This document summarizes research on genome editing in poultry. It discusses how gene editing could help address issues like disease resilience and food allergies in chickens. The researchers have used CRISPR-Cas9 to successfully edit genes in chicken primordial germ cells (PGCs) through direct injection. This led to heterozygous and homozygous gene deletions being passed down to subsequent generations. Applications mentioned include deleting allergenic proteins from eggs and improving resistance to avian influenza. The document acknowledges the team conducting this research and expresses hope that their work can enhance sustainability, health, and efficiency in poultry production while improving food safety.
Gene editing with CRISPR/Cas9: sorghum as a case studyapaari
This document summarizes a presentation on using CRISPR/Cas9 gene editing to improve sorghum. The presentation discusses using gene editing to increase grain size and protein content in sorghum, which could improve its use for animal feed. It describes ongoing research knocking out specific genes to increase grain size by over 10% and protein content by up to 24%. If successful, this could increase sorghum yields and protein per hectare for uses like poultry feed. The presentation notes that gene edited crops may not be classified as GMOs, depending on regulatory decisions, and outlines ongoing research using this technology in sorghum.
Base editing is being used to induce precise mutations in rice in order to accelerate crop improvement. Researchers developed a base editing-mediated gene evolution method to diversify the sequence of the rice acetolactate synthase 1 (OsALS1) gene, which codes for the target of herbicide resistance. Multiple sgRNAs were used to introduce mutations across the OsALS1 locus. Novel mutations were identified that conferred resistance to the herbicide bispyribac-sodium. The resistant mutation was then introduced into an elite rice cultivar through base editing to generate a new herbicide tolerant variety. This demonstrates how base editing can be used to artificially evolve genes and introduce beneficial traits into commercial crops.
Need to revolutionize the crop breedingamoldchokhat
Mankind is facing an enormous challenge of food insecurity. By the year 2050, the population of the world is projected to increase by 35% to a whopping 9 billion; and an almost doubling of global food production is needed to feed the planet. This additional food for humans and farm animals has to come from the existing land, through maximization of genetic potential and relatively quickly. This demand for unprecedented productivity in agriculture needs to be realized in the presence of growing challenges of climate change, shortsighted land-use practices and increasing cost of agriculture despite the rate of improved adoption of technology in crop breeding. Recent advances in our understanding of genes and genomes combined with development of novel tools in biotechnology will play a vital role in accelerating efforts in plant breeding. Genomics assisted breeding assists the breeders in precise selection to enhance the effectivity and enhancement of the precise selection to develop a new cultivars.
CRISPR-Cas is a genome editing technique derived from bacterial immune systems that allows for precise genomic modifications. The document discusses applications of CRISPR-Cas in plants, animals, and bacteria, including developing pest and disease resistant crops and livestock, modifying stem cells and embryos, targeting antibiotic resistant bacteria, and controlling gene expression.
Genetic engineering is the process of manipulating genes to introduce desirable traits. It involves combining DNA from different organisms, such as inserting a gene for insulin into bacteria. The gene is inserted into a plasmid or virus vector and introduced into a host cell. This allows the production of proteins like insulin to treat diseases. While genetic engineering holds promise to treat diseases, some argue it could disrupt nature in unintended ways. Regulatory issues also exist regarding its applications and effects.
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increa...apaari
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increased crop productivity by MK Reddy during the Regional Expert Consultation on Gene Editing in Agriculture and its Regulations Technical Session III
This presentation discusses genetic engineering and was presented by a group of 4 students in the Environmental Science department. It defines genetic engineering as manually adding new DNA to an organism. It provides examples of genetically engineered plants and discusses the history and basic concepts of genetic engineering. The presentation explains the process of genetic engineering including extracting DNA from one organism and inserting it into another. It compares genetic engineering to traditional breeding and discusses applications like transgenic organisms and cloning.
This document summarizes information about CircoFLEX, a PCV2 vaccine produced by Boehringer Ingelheim using their PCA TM and Impran FLEX TM technologies. It discusses results from trials showing CircoFLEX was effective at reducing mortality and increasing weight gain when given to pigs at 21 and 42 days of age. It also summarizes results from multiple trials and field studies demonstrating the benefits of CircoFLEX compared to other PCV2 vaccines when given as a single dose at 3 weeks of age.
Application of genome editing in farm animals: Cattle - Alison Van EenennaamOECD Environment
This document summarizes an expert presentation on animal genomics and biotechnology education. It discusses:
1) Cattle contribute significantly to global animal protein supply and demand for cattle products is projected to increase substantially by 2050. Accelerating genetic gain through breeding programs is needed to meet this demand more sustainably.
2) Genome editing holds promise for introducing beneficial traits into cattle, such as polledness, heat tolerance, and disease resistance. One example discussed was using TALENs to introduce the polled allele into dairy cattle to eliminate painful horn removal.
3) However, regulatory hurdles like the FDA's stance that gene-edited animals are drugs could slow the application of new gene editing
Plant-produced subviral HBV particles as carriers for antigen protein epitope...MarcinCzyz
Presentation of a scientific research project - expression of a fusion proteins in plants - carrier structure for immunogenic epitopes, for the purpose of oral vaccine, but also for potential purification and traditional vaccine.
Genetics engineering is the technology for modifying the genetics information in a plant, animal or human in order to produce some desired trait or characteristic
This document discusses genome editing in fruit crops using CRISPR/Cas9 technology. It provides examples of using CRISPR to edit genes involved in fruit ripening, pigmentation, and flowering time regulation in strawberry, banana, apple, and kiwifruit. Specifically, it describes using CRISPR to increase beta-carotene levels in banana, induce early flowering in apple and pear, and generate dwarf kiwifruit plants. The document concludes that integrating biotechnology like CRISPR with conventional breeding is a promising strategy for fruit crop improvement.
Deciphering the Dynamic Coupling of the Human Immune System and the Gut Micro...Larry Smarr
This document discusses Dr. Larry Smarr's research into understanding the relationship between the human immune system and gut microbiome in Crohn's disease. Dr. Smarr sequenced his own genome to identify genetic polymorphisms associated with higher risk of Crohn's disease. He also conducted fine-time resolution sampling to study the distinct dynamics of the innate and adaptive immune system in health and disease. Additionally, he found major shifts in the gut microbiome between healthy individuals and those with two forms of inflammatory bowel disease.
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 discusses the use of CRISPR gene editing technology. It provides examples of how CRISPR has been used to cure diseases in animals and potentially humans, create customized cancer models and modify animal organs. It also describes how CRISPR can be applied in agriculture to develop drought-resistant and pest-resistant crops, as well as in industrial biotechnology settings. The document then explains how gene drives work to alter genes and spread them through populations using CRISPR. It calls for responsible development of this technology through community guidance, transparency and democratic decision making.
This study aims to determine if there is a relationship between ploidy number and branching patterns in big sagebrush (Artemisia tridentata ssp. tridentata). Sage-grouse prefer to nest in U-shaped branching that is found in big sagebrush. However, some burned areas have regrown with V-shaped branching instead. The focus is on using flow cytometry to analyze the ploidy (number of sets of chromosomes) of sagebrush samples. Preliminary results found a nuclear DNA content lower than expected, possibly due to cell wall material interfering. Further optimization of the nuclei isolation procedure is needed to accurately determine ploidy levels and investigate impacts on branching patterns.
Genetic engineering can help address problems like food shortages by developing crops resistant to threats. The Philippines faces a rice shortage due to black bug infestation. A company has developed weevil-resistant corn through genetic engineering that could help if planted there. However, genetic engineering also presents risks that must be considered, like potential health or environmental impacts, before pursuing this solution. Experts would need to evaluate what traits were modified in the corn, the benefits and risks of genetic engineering, and whether the benefits outweigh the risks.
The document discusses genetic engineering and genetically modified organisms (GMOs). It defines genetic engineering as the direct modification of an organism's genome through techniques like inserting, replacing or removing genes. This allows scientists to modify traits. Some key points:
- The first GMOs were bacteria in 1973, mice in 1974, and commercial GMO development began with insulin-producing bacteria in 1982.
- Common GMO crops include 93% of soybeans, 93% of cotton and 86% of corn grown in the US. One example is Bt-corn which produces a toxin harmful to insects.
- GMOs can be engineered for traits like insect or herbicide resistance, increased yield, or improved nutrition. Concer
This document provides an overview of cisgenesis, which involves genetically modifying a plant with a natural gene from a sexually compatible plant species. It defines cisgenesis and provides examples of cisgenic crops. It discusses the limitations of traditional breeding and transgenesis, and how cisgenesis addresses some of these limitations. The document outlines the process for developing cisgenic plants, including gene isolation, vector construction, transformation and selection methods. It summarizes a case study on developing cisgenic apple with scab resistance. Finally, it discusses opportunities and challenges for the future of cisgenesis.
1) The document discusses the coevolutionary struggle between plants and pathogens, with pathogens secreting effector proteins that suppress plant immunity and plants evolving resistance genes to detect effectors.
2) Sequencing of the P. sojae genome revealed a huge superfamily of over 400 effector-like genes that show signs of accelerated divergence, likely due to coevolutionary conflict with plant hosts.
3) Analysis of P. sojae transcriptomes showed that a small number of effector genes contribute most transcripts during infection, suggesting a few key effectors have disproportionate importance for virulence.
Need to revolutionize the crop breedingamoldchokhat
Mankind is facing an enormous challenge of food insecurity. By the year 2050, the population of the world is projected to increase by 35% to a whopping 9 billion; and an almost doubling of global food production is needed to feed the planet. This additional food for humans and farm animals has to come from the existing land, through maximization of genetic potential and relatively quickly. This demand for unprecedented productivity in agriculture needs to be realized in the presence of growing challenges of climate change, shortsighted land-use practices and increasing cost of agriculture despite the rate of improved adoption of technology in crop breeding. Recent advances in our understanding of genes and genomes combined with development of novel tools in biotechnology will play a vital role in accelerating efforts in plant breeding. Genomics assisted breeding assists the breeders in precise selection to enhance the effectivity and enhancement of the precise selection to develop a new cultivars.
CRISPR-Cas is a genome editing technique derived from bacterial immune systems that allows for precise genomic modifications. The document discusses applications of CRISPR-Cas in plants, animals, and bacteria, including developing pest and disease resistant crops and livestock, modifying stem cells and embryos, targeting antibiotic resistant bacteria, and controlling gene expression.
Genetic engineering is the process of manipulating genes to introduce desirable traits. It involves combining DNA from different organisms, such as inserting a gene for insulin into bacteria. The gene is inserted into a plasmid or virus vector and introduced into a host cell. This allows the production of proteins like insulin to treat diseases. While genetic engineering holds promise to treat diseases, some argue it could disrupt nature in unintended ways. Regulatory issues also exist regarding its applications and effects.
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increa...apaari
Editing rice-genome with CRISPR/Cas9: To improve agronomic traits for increased crop productivity by MK Reddy during the Regional Expert Consultation on Gene Editing in Agriculture and its Regulations Technical Session III
This presentation discusses genetic engineering and was presented by a group of 4 students in the Environmental Science department. It defines genetic engineering as manually adding new DNA to an organism. It provides examples of genetically engineered plants and discusses the history and basic concepts of genetic engineering. The presentation explains the process of genetic engineering including extracting DNA from one organism and inserting it into another. It compares genetic engineering to traditional breeding and discusses applications like transgenic organisms and cloning.
This document summarizes information about CircoFLEX, a PCV2 vaccine produced by Boehringer Ingelheim using their PCA TM and Impran FLEX TM technologies. It discusses results from trials showing CircoFLEX was effective at reducing mortality and increasing weight gain when given to pigs at 21 and 42 days of age. It also summarizes results from multiple trials and field studies demonstrating the benefits of CircoFLEX compared to other PCV2 vaccines when given as a single dose at 3 weeks of age.
Application of genome editing in farm animals: Cattle - Alison Van EenennaamOECD Environment
This document summarizes an expert presentation on animal genomics and biotechnology education. It discusses:
1) Cattle contribute significantly to global animal protein supply and demand for cattle products is projected to increase substantially by 2050. Accelerating genetic gain through breeding programs is needed to meet this demand more sustainably.
2) Genome editing holds promise for introducing beneficial traits into cattle, such as polledness, heat tolerance, and disease resistance. One example discussed was using TALENs to introduce the polled allele into dairy cattle to eliminate painful horn removal.
3) However, regulatory hurdles like the FDA's stance that gene-edited animals are drugs could slow the application of new gene editing
Plant-produced subviral HBV particles as carriers for antigen protein epitope...MarcinCzyz
Presentation of a scientific research project - expression of a fusion proteins in plants - carrier structure for immunogenic epitopes, for the purpose of oral vaccine, but also for potential purification and traditional vaccine.
Genetics engineering is the technology for modifying the genetics information in a plant, animal or human in order to produce some desired trait or characteristic
This document discusses genome editing in fruit crops using CRISPR/Cas9 technology. It provides examples of using CRISPR to edit genes involved in fruit ripening, pigmentation, and flowering time regulation in strawberry, banana, apple, and kiwifruit. Specifically, it describes using CRISPR to increase beta-carotene levels in banana, induce early flowering in apple and pear, and generate dwarf kiwifruit plants. The document concludes that integrating biotechnology like CRISPR with conventional breeding is a promising strategy for fruit crop improvement.
Deciphering the Dynamic Coupling of the Human Immune System and the Gut Micro...Larry Smarr
This document discusses Dr. Larry Smarr's research into understanding the relationship between the human immune system and gut microbiome in Crohn's disease. Dr. Smarr sequenced his own genome to identify genetic polymorphisms associated with higher risk of Crohn's disease. He also conducted fine-time resolution sampling to study the distinct dynamics of the innate and adaptive immune system in health and disease. Additionally, he found major shifts in the gut microbiome between healthy individuals and those with two forms of inflammatory bowel disease.
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 discusses the use of CRISPR gene editing technology. It provides examples of how CRISPR has been used to cure diseases in animals and potentially humans, create customized cancer models and modify animal organs. It also describes how CRISPR can be applied in agriculture to develop drought-resistant and pest-resistant crops, as well as in industrial biotechnology settings. The document then explains how gene drives work to alter genes and spread them through populations using CRISPR. It calls for responsible development of this technology through community guidance, transparency and democratic decision making.
This study aims to determine if there is a relationship between ploidy number and branching patterns in big sagebrush (Artemisia tridentata ssp. tridentata). Sage-grouse prefer to nest in U-shaped branching that is found in big sagebrush. However, some burned areas have regrown with V-shaped branching instead. The focus is on using flow cytometry to analyze the ploidy (number of sets of chromosomes) of sagebrush samples. Preliminary results found a nuclear DNA content lower than expected, possibly due to cell wall material interfering. Further optimization of the nuclei isolation procedure is needed to accurately determine ploidy levels and investigate impacts on branching patterns.
Genetic engineering can help address problems like food shortages by developing crops resistant to threats. The Philippines faces a rice shortage due to black bug infestation. A company has developed weevil-resistant corn through genetic engineering that could help if planted there. However, genetic engineering also presents risks that must be considered, like potential health or environmental impacts, before pursuing this solution. Experts would need to evaluate what traits were modified in the corn, the benefits and risks of genetic engineering, and whether the benefits outweigh the risks.
The document discusses genetic engineering and genetically modified organisms (GMOs). It defines genetic engineering as the direct modification of an organism's genome through techniques like inserting, replacing or removing genes. This allows scientists to modify traits. Some key points:
- The first GMOs were bacteria in 1973, mice in 1974, and commercial GMO development began with insulin-producing bacteria in 1982.
- Common GMO crops include 93% of soybeans, 93% of cotton and 86% of corn grown in the US. One example is Bt-corn which produces a toxin harmful to insects.
- GMOs can be engineered for traits like insect or herbicide resistance, increased yield, or improved nutrition. Concer
This document provides an overview of cisgenesis, which involves genetically modifying a plant with a natural gene from a sexually compatible plant species. It defines cisgenesis and provides examples of cisgenic crops. It discusses the limitations of traditional breeding and transgenesis, and how cisgenesis addresses some of these limitations. The document outlines the process for developing cisgenic plants, including gene isolation, vector construction, transformation and selection methods. It summarizes a case study on developing cisgenic apple with scab resistance. Finally, it discusses opportunities and challenges for the future of cisgenesis.
1) The document discusses the coevolutionary struggle between plants and pathogens, with pathogens secreting effector proteins that suppress plant immunity and plants evolving resistance genes to detect effectors.
2) Sequencing of the P. sojae genome revealed a huge superfamily of over 400 effector-like genes that show signs of accelerated divergence, likely due to coevolutionary conflict with plant hosts.
3) Analysis of P. sojae transcriptomes showed that a small number of effector genes contribute most transcripts during infection, suggesting a few key effectors have disproportionate importance for virulence.
Genome to pangenome : A doorway into crops genome explorationKiranKm11
This seminar underpins the significance and need of formulating pan-genome oriented crop improvement strategies over single reference genome based studies. Pangenome graphs uncovers large repository of genetic variation which could we useful for planning and executing strategic crop improvement programmed
This presentation discusses novel technologies to study the resistome, which is the collection of antibiotic resistance genes found in an environment. It describes culture-based and culture-independent methods to analyze the resistome, including metagenomic shotgun sequencing, functional metagenomics, and high-throughput quantitative PCR. The presentation also details a study that used these methods to analyze the gut resistome of ICU patients receiving intensive antibiotic therapy and found a rich diversity of resistance genes that increased during their hospital stay. Long-read nanopore sequencing is also presented as an upcoming method to map resistomes by linking resistance genes to mobile genetic elements.
This document provides an overview of edible vaccines. It discusses how edible vaccines are produced by introducing genes encoding vaccine antigens into edible plants using transformation methods. The document outlines various plant species used for edible vaccines like tomatoes, rice, maize, potatoes, and tobacco. It discusses factors affecting the efficacy of edible vaccines and provides examples of edible vaccine research for diseases like malaria, measles, hepatitis B, norovirus, and Alzheimer's disease. The conclusion states that edible vaccines could improve vaccination programs in developing countries by reducing costs and need for cold storage.
JGI: Genome size impacts on plant adaptationjrossibarra
Genome size may impact how plant genomes adapt, offering larger mutational targets leading to more adaptation from standing variation and more adaptation in noncoding regions.
This document summarizes Jai Kishan's presentation on gene manipulation techniques. It discusses conventional plant breeding, mutation breeding, transgenic plants, and several precise gene editing techniques like ZFN, TALENs, and CRISPR-Cas9. CRISPR-Cas systems provide adaptive immunity in bacteria and archaea by recognizing foreign DNA. The document then reviews the history and components of the CRISPR-Cas system and its applications in cancer therapy, viral diseases, bacterial infections, and genetic disorders. It also discusses challenges like delivery methods, mosaicism, immune responses, and off-target mutations. Key references on the discovery of CRISPR and its use in agriculture and as a genetic manipulation tool are presented.
This document summarizes research on cloning and expression analysis of rice genes involved in infection with the rice nematode Hirschmaniella oryzae. Key points include:
- Six rice genes were selected based on previous expression data under H. oryzae infection. These genes were cloned from rice roots.
- An infection experiment was conducted where rice seedlings were infected with nematodes at different time points. Gene expression was analyzed using qPCR.
- Preliminary results found three genes - Cupin, Membrane, and B-box - had expression patterns consistent with previous data under H. oryzae infection. Further research is suggested to understand the roles of these genes in rice-
Marker assisted selection of male sterility in rice --vipin Vipin Kannan
This document provides information on various methods of inducing male sterility in plants, especially rice, for the purpose of hybrid seed production. It discusses chemical, genetic, and transgenic approaches. Specifically, it describes cytoplasmic male sterility (CMS), nuclear male sterility (NMS), and cytoplasmic-genetic male sterility (CGMS). It also discusses the use of marker-assisted selection (MAS) to more efficiently select for male sterility genes and introgress them into adapted varieties through techniques like marker-assisted backcrossing (MAB). Overall, the document outlines methods for inducing and tracking male sterility that can facilitate efficient hybrid rice breeding programs.
This document summarizes research on advances in plant breeding systems. It discusses how modern tools like molecular markers, marker-assisted selection, genomic selection, and new statistical methods are being used along with technologies like RNA interference, CRISPR/Cas9, and TALENs to introduce beneficial genes and improve traits. Specific examples discussed include research on improving okra and rice varieties for traits like disease resistance and yield through techniques like tissue culture, molecular characterization, and genome editing. The document also summarizes research on inducing mutations in wheat using chemicals like EMS to generate genetic variability for breeding programs.
Applying agricultural biotechnology tools and capabilities to enhance food se...ExternalEvents
Applying agricultural biotechnology tools and capabilities to enhance food security and nutrition from local food crops to stimulate sustainable income opportunities for small holder farmers to reduce poverty presentation by "Howard-Yana Shapiro, Mars Incorporated, Dranesville and
University of California Davis, Davis, United States of America"
Plant disease resistance genes: current status and future directions.RonikaThakur
Agriculture plays a key role to ensure the food security. But plant diseases hinder the crop production by reducing yield to much extent. To overcome this problem it is crucial to understand plant disease resistance genes which prevent growth of plant pathogens thereby reducing the yield loss.
CD Genomics is dedicated to providing a comprehensive list of genomics and microarray solutions for agriculture, including genome, exome, transcriptome, and metagenome sequencing, genome-wide association studies (GWAS), and targeted sequencing and genotyping that focus on a subset of regions or genes such as single nucleotide polymorphisms (SNPs). https://www.cd-genomics.com/Transcriptomics.html
Advances in genetic basis for animal diseasesRitasree Sarma
Genetic resistance and tolerance in animals can help address issues with traditional disease control methods like drugs. Genetic factors contribute to an animal's ability to resist a pathogen. Researchers study genetic resistance at species, breed, and individual levels. Identifying genetic markers and polymorphisms associated with resistance can help breed disease-resistant animals through selection. Approaches include transgenic modification to introduce resistance genes and genome editing to modify endogenous genes. Future work involves functional genomics to further understand host-pathogen interactions and develop new disease management strategies.
This document summarizes research on advances in plant breeding systems. It discusses how biotechnology tools can help overcome limitations in crop production by improving quantity, quality, and stress tolerance. Molecular markers, marker-assisted selection, genomic selection, and new statistical tools are supporting conventional breeding. Other technologies discussed include standardized field sites, high-throughput phenotyping, DH lines, and various analytical techniques. The document also discusses using tools like CRISPR/Cas9 and RNAi for genetic engineering to introduce beneficial genes. Specific research on okra and rice breeding is summarized, including studies on tissue culture, induced mutations, and marker-assisted selection.
Dr. Jack Dekkers - Using genetic selection and genomics to combat infectious ...John Blue
Using genetic selection and genomics to combat infectious disease - Dr. Jack Dekkers, Iowa State University, from the 2017 North American PRRS/National Swine Improvement Federation Joint Meeting, December 1‐3, 2017, Chicago, Illinois, USA.
More presentations at http://www.swinecast.com/2017-north-american-prrs-nsif-joint-meeting
This document summarizes the potential of RNA interference (RNAi) technology for crop improvement. It discusses how RNAi was discovered through early experiments in plants in the 1990s. The mechanism of RNAi involves long double-stranded RNA being cleaved by an enzyme called Dicer into small interfering RNAs (siRNAs) that are incorporated into a protein complex called RISC that targets and degrades complementary mRNAs, preventing gene expression. The document outlines several successful applications of RNAi technology for increasing biotic stress tolerance in crops against viruses, bacteria, fungi and insects by silencing key pathogen genes. It also discusses using RNAi to modify other crop traits like nutritional quality and abiotic stress resistance.
From Lab to Plate: Harnessing Plant Genetic Engineering for Resilient and Sus...AchyutaBasak
With the ongoing expansion of the global population, the issues around food security, environmental sustainability, and resource scarcity are becoming progressively more urgent, and genetic engineering emerges as a powerful tool for sustainable agriculture. Breeders have been able to produce improved varieties, like improvement of different yield and yield attributing traits of many crops by conventional breeding methods; however, numerous obstacles persist, and the advent of new technologies holds promise for tackling these hurdles. The area of crop improvement has been transformed by developments in genetic engineering technology, which have opened up previously unimaginable prospects to increase agricultural productivity, sustainability, and resilience.
This presentation seeks to provide a comprehensive study of the key concepts and methodologies associated with genetic engineering, including prominent tools such as zinc finger nucleases CRISPR-Cas9 and TALENs. It also explores the several approaches used to manipulate crop genomes, including agrobacterium-assisted gene transfer and particle bombardment techniques, emphasizing their advantages. The use of advanced genetic engineering technology has helped identify new features and emerged as a crucial factor in ensuring food security. In addition, this chapter also examines the specific use of genetic engineering in improving agricultural crops. We explore the potential for accurate and focused modifications to impart desirable traits, such as tolerance to biotic and abiotic stresses, enhanced nutritional value, and increased yield. Additionally, we emphasise the distinct genes and proteins involved in conferring these traits. This chapter discusses the potential implications of CRISPR-Cas9 technology for enhancing various qualities. In this context, we further examine the capacity of genetic engineering to bring about significant changes in relation to worldwide issues such as climate change, food security, and sustainability.
Functional genomics is a general approach toward understanding how the genes of an organism work together by assigning new functions to unknown genes. Information about the hypothesized function of an unknown gene may be deduced from its sequence structure using already known functions of similar genes as the basis for comparison. Gene function analysis therefore necessitates the analysis of temporal and spatial gene expression patterns (Yunbi Xu et al , Plant Molecular Biology (2005) ).
Similar to Plant health emergencies in the face of a changing environment (20)
Don’t perish! A step by step guide to writing a scientific paperSophien Kamoun
Sophien Kamoun's presentation to the Norwich research Park PhD student. A step by step guide to writing scientific papers. April 1, 2020.
This presentation is part of a workshop about writing scientific papers. It describes a 10 step guide for writing papers.
1. Create a folder
2. Write a story line
3. Make list of Figures
4. Finalize Figures
5. Write the Results
6. Write the Intro
7. Write the Discussion
8. Assemble the Abstract
9. Write the Title
10. Post it on bioRxiv
Faites de la Science: Mes aventures de BiologisteSophien Kamoun
Science Festival in Tunis “Fête de la science Tunisie” at the cité des Sciences de Tunis with my presentation “Faites de la Science: Mes aventures de Biologiste.”
Everything you wanted to know about research integrity but never dared to askSophien Kamoun
Everything you wanted to know about research integrity but never dared to ask discusses research misconduct, standards of professional conduct, and principles of good research practice. It defines research misconduct as misrepresentation, falsification, or fabrication of data. While honest errors are not misconduct, failure to address errors could be. The importance of admitting when one is wrong and making timely corrections is emphasized. Research integrity is supported by high professional standards, good practices, appropriate oversight systems, and a culture of open discussion.
The document discusses the research interests and vision of the Kamoun Lab, which aims to integrate evolutionary and mechanistic approaches to studying plant-microbe interactions. Specifically, the lab seeks to understand how pathogens evolve and adapt following host jumps, and how plants evolve immune responses and disease resistance. The lab uses various plant and pathogen systems combined with skills such as protein analysis, genome sequencing, CRISPR, and microscopy to answer questions about how pathogens traffic effectors into cells and how plants recognize effectors with NLR sensors.
The Edge of Tomorrow — Plant Health in the 21st CenturySophien Kamoun
Presented at the ICPP2018 International Congress of Plant Pathology Plenary Session - Plant Health is Earth’s Wealth, Monday, July 30, 2018. See notes and acknowledgments at http://kamounlab.tumblr.com/post/176385835530/the-edge-of-tomorrow-plant-health-in-the-21st
From sequence to phenotype: Functional genomics of the oomycete PhytophthoraSophien Kamoun
Sophien Kamoun's talk at the 2002 Gordon Research Conference "Cellular and Molecular Mycology", June 16-21, Holderness School, New Hampshire, USA. https://www.grc.org/cellular-and-molecular-mycology-conference/2002/
Pathogenomics of emerging plant pathogens: too little, too lateSophien Kamoun
This document discusses the threat posed by emerging plant pathogens to global food security. It notes how the potato late blight pathogen caused the Irish potato famine and continues to cause devastating crop losses. The emergence and spread of new, aggressive lineages of plant pathogens like the "blue 13" lineage of Phytophthora infestans can outcompete other lineages and overcome plant resistance. Genomic analysis of the invasive "blue 13" lineage revealed genetic changes in effector genes that enhance its virulence and allow it to infect potato cultivars. However, this lineage possesses effectors that are targets of plant immune receptors, indicating potential strategies for deploying genetic resistance. The document stresses the importance of rapidly sequencing pathogen genomes to inform management of
"Keeping up with the plant destroyers." My talk at The Royal Society, 7 March...Sophien Kamoun
Tackling emerging threats to animal health, food security and ecosystem resilience, The Royal Society, Monday 7 – Tuesday 8 March 2016. https://royalsociety.org/events/2016/03/emerging-fungal-threats/
Sophien's lectures on Oomycetes, UEA BIO 6007B, January 2016Sophien Kamoun
This document discusses the genome of the oomycete Phytophthora infestans, the causal agent of potato late blight. It finds that the P. infestans genome is large, containing many repetitive elements. It has expanded protein families related to pathogenesis, including hundreds of effector proteins similar to known avirulence genes. Comparison to the P. ramorum genome showed the two species genomes have diverged, with rapid expansion and diversification of gene families for plant infection mechanisms. This supports an evolutionary history of these oomycete pathogens adapting through genomic changes to infect different host plants.
Everything you wanted to know about research integrity...Sophien Kamoun
...but never dared to ask
Presented at the Norwich Research Park, October 2, 2015.
Notes about this talk are at http://kamounlab.tumblr.com/post/130328881710/everything-you-wanted-to-know-about-research
This document summarizes key findings from the genome sequencing of the oomycete plant pathogen Magnaporthe grisea, which causes rice blast disease. Some key points:
- The draft genome sequence was 38.8 megabases in length and contained a large number of genes encoding secreted proteins and carbohydrate-binding domains that help the pathogen infect plants.
- The genome also contained an expanded family of G-protein coupled receptors and many genes involved in secondary metabolism, both of which are important for fungal pathogenesis.
- Expression of several of these genes increased during early infection, suggesting they play a role in M. grisea's ability to infect rice plants and cause disease.
My talk to the PhD students NRP at the Doctoral Training Programme Summer Conference 2015, The Assembly House, Norwich, Thursday 18th June.
Notes and acknowledgments at http://kamounlab.tumblr.com/post/121748816600/what-are-world-class-science-outputs
PPT on Alternate Wetting and Drying presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
(June 12, 2024) Webinar: Development of PET theranostics targeting the molecu...Scintica Instrumentation
Targeting Hsp90 and its pathogen Orthologs with Tethered Inhibitors as a Diagnostic and Therapeutic Strategy for cancer and infectious diseases with Dr. Timothy Haystead.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
Authoring a personal GPT for your research and practice: How we created the Q...Leonel Morgado
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
The debris of the ‘last major merger’ is dynamically youngSérgio Sacani
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Anti-Universe And Emergent Gravity and the Dark UniverseSérgio Sacani
Recent theoretical progress indicates that spacetime and gravity emerge together from the entanglement structure of an underlying microscopic theory. These ideas are best understood in Anti-de Sitter space, where they rely on the area law for entanglement entropy. The extension to de Sitter space requires taking into account the entropy and temperature associated with the cosmological horizon. Using insights from string theory, black hole physics and quantum information theory we argue that the positive dark energy leads to a thermal volume law contribution to the entropy that overtakes the area law precisely at the cosmological horizon. Due to the competition between area and volume law entanglement the microscopic de Sitter states do not thermalise at sub-Hubble scales: they exhibit memory effects in the form of an entropy displacement caused by matter. The emergent laws of gravity contain an additional ‘dark’ gravitational force describing the ‘elastic’ response due to the entropy displacement. We derive an estimate of the strength of this extra force in terms of the baryonic mass, Newton’s constant and the Hubble acceleration scale a0 = cH0, and provide evidence for the fact that this additional ‘dark gravity force’ explains the observed phenomena in galaxies and clusters currently attributed to dark matter.
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 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.
Sexuality - Issues, Attitude and Behaviour - Applied Social Psychology - Psyc...PsychoTech Services
A proprietary approach developed by bringing together the best of learning theories from Psychology, design principles from the world of visualization, and pedagogical methods from over a decade of training experience, that enables you to: Learn better, faster!
JAMES WEBB STUDY THE MASSIVE BLACK HOLE SEEDSSérgio Sacani
The pathway(s) to seeding the massive black holes (MBHs) that exist at the heart of galaxies in the present and distant Universe remains an unsolved problem. Here we categorise, describe and quantitatively discuss the formation pathways of both light and heavy seeds. We emphasise that the most recent computational models suggest that rather than a bimodal-like mass spectrum between light and heavy seeds with light at one end and heavy at the other that instead a continuum exists. Light seeds being more ubiquitous and the heavier seeds becoming less and less abundant due the rarer environmental conditions required for their formation. We therefore examine the different mechanisms that give rise to different seed mass spectrums. We show how and why the mechanisms that produce the heaviest seeds are also among the rarest events in the Universe and are hence extremely unlikely to be the seeds for the vast majority of the MBH population. We quantify, within the limits of the current large uncertainties in the seeding processes, the expected number densities of the seed mass spectrum. We argue that light seeds must be at least 103 to 105 times more numerous than heavy seeds to explain the MBH population as a whole. Based on our current understanding of the seed population this makes heavy seeds (Mseed > 103 M⊙) a significantly more likely pathway given that heavy seeds have an abundance pattern than is close to and likely in excess of 10−4 compared to light seeds. Finally, we examine the current state-of-the-art in numerical calculations and recent observations and plot a path forward for near-future advances in both domains.
12. Hybridization
Introgression
Mutagenesis
Transgenics
etc.
Ever since Mendel—Crop genetic improvement
Gene editing – the ultimate in precision is to
replace one of a few letters in the genome