Update on the assembly and annotation of the blueberry genomeRob Reid
Update and description of the blueberry genome. Describes annotation process of using gage and pathview to identify key pathways detected in the genome.
METABOLIC PROFILING OF RIPENING STRAWBERRY (Fragaria x ananassa)Ashlyn Wedde
Strawberries were analyzed to understand how metabolite profiles differ between cultivars and tissue types during ripening. Four strawberry cultivars (Festival, Sensation, Winterstar, Radiance) had receptacle and achene tissue separated at six ripening stages, from small green to ripe. Metabolites were investigated using GC-MS and UPLC-qTOF-MS profiling. Correlation analysis showed cluster patterns between metabolite profiles in cultivars and tissues. Certain metabolites, like ellagic acid, differed significantly between cultivars and tissues throughout ripening. Understanding these metabolic differences provides insights into fruit quality traits and health benefits between strawberry cultivars.
RNA-Seq analysis of blueberry fruit identifies candidate genes involved in ri...Ann Loraine
I presented these slides at the Plant Metabolic Network workshop held at the Plant Animal Genome Conference (PAG) XXII, January, 2014. The main goals of the talk were to describe RNA-Seq based annotation of a blueberry genome assembly and explain how we used PlantCyc enzyme data to associate blueberry genes with metabolic pathways.
This document summarizes the history and applications of RNA interference (RNAi) and microRNAs (miRNAs) in plants. It discusses how small RNAs guide regulatory processes, how dicer and argonauts are involved, and some of the early discoveries in RNAi from the 1990s onward. It then lists several applications of RNAi/miRNAs in plants, such as improving traits like biomass, yield, stress resistance, and nutrition. Specific examples are given of overexpressing miRNAs like miR156 to increase biomass and yield in maize and rice. In conclusion, RNAi/miRNAs can be powerful tools for improving important agricultural traits in plants.
DNA methylation patterns undergo significant changes during development. In early development, methylation patterns are erased through both active and passive demethylation. After implantation, de novo methylation establishes new patterns mediated by DNMT3A and DNMT3B. Tissue-specific methylation then arises from both protection of CpG islands and targeted demethylation of specific genes in different tissues. Polycomb complexes play a role in targeting de novo methylation during development.
Epigenetics is the study of inheritable changes that occur without altering the DNA sequence. These changes include modifications to gene expression and phenotypes through mechanisms other than the DNA sequence, such as environmental factors. Epigenetic changes can be caused by an individual's choices and environment and can potentially affect their children and grandchildren. Identical twins with the same DNA but different environments and lifestyles can have different epigenetic profiles and health outcomes due to factors like stress levels and diet. While epigenetics research holds promise, it also raises ethical concerns and can potentially cause abnormalities if not carefully studied.
This document provides tips and strategies for effective scientific writing. It discusses structuring papers, using outlines and reverse outlines, paragraph structure with topic sentences, polishing and revising with plain language, ethics of writing and figure preparation, setting aside time for writing, and not letting good data be explained poorly through bad writing. It also covers writing micro-articles, determining significance, using active voice, nominalizations, and sentence structure.
Update on the assembly and annotation of the blueberry genomeRob Reid
Update and description of the blueberry genome. Describes annotation process of using gage and pathview to identify key pathways detected in the genome.
METABOLIC PROFILING OF RIPENING STRAWBERRY (Fragaria x ananassa)Ashlyn Wedde
Strawberries were analyzed to understand how metabolite profiles differ between cultivars and tissue types during ripening. Four strawberry cultivars (Festival, Sensation, Winterstar, Radiance) had receptacle and achene tissue separated at six ripening stages, from small green to ripe. Metabolites were investigated using GC-MS and UPLC-qTOF-MS profiling. Correlation analysis showed cluster patterns between metabolite profiles in cultivars and tissues. Certain metabolites, like ellagic acid, differed significantly between cultivars and tissues throughout ripening. Understanding these metabolic differences provides insights into fruit quality traits and health benefits between strawberry cultivars.
RNA-Seq analysis of blueberry fruit identifies candidate genes involved in ri...Ann Loraine
I presented these slides at the Plant Metabolic Network workshop held at the Plant Animal Genome Conference (PAG) XXII, January, 2014. The main goals of the talk were to describe RNA-Seq based annotation of a blueberry genome assembly and explain how we used PlantCyc enzyme data to associate blueberry genes with metabolic pathways.
This document summarizes the history and applications of RNA interference (RNAi) and microRNAs (miRNAs) in plants. It discusses how small RNAs guide regulatory processes, how dicer and argonauts are involved, and some of the early discoveries in RNAi from the 1990s onward. It then lists several applications of RNAi/miRNAs in plants, such as improving traits like biomass, yield, stress resistance, and nutrition. Specific examples are given of overexpressing miRNAs like miR156 to increase biomass and yield in maize and rice. In conclusion, RNAi/miRNAs can be powerful tools for improving important agricultural traits in plants.
DNA methylation patterns undergo significant changes during development. In early development, methylation patterns are erased through both active and passive demethylation. After implantation, de novo methylation establishes new patterns mediated by DNMT3A and DNMT3B. Tissue-specific methylation then arises from both protection of CpG islands and targeted demethylation of specific genes in different tissues. Polycomb complexes play a role in targeting de novo methylation during development.
Epigenetics is the study of inheritable changes that occur without altering the DNA sequence. These changes include modifications to gene expression and phenotypes through mechanisms other than the DNA sequence, such as environmental factors. Epigenetic changes can be caused by an individual's choices and environment and can potentially affect their children and grandchildren. Identical twins with the same DNA but different environments and lifestyles can have different epigenetic profiles and health outcomes due to factors like stress levels and diet. While epigenetics research holds promise, it also raises ethical concerns and can potentially cause abnormalities if not carefully studied.
This document provides tips and strategies for effective scientific writing. It discusses structuring papers, using outlines and reverse outlines, paragraph structure with topic sentences, polishing and revising with plain language, ethics of writing and figure preparation, setting aside time for writing, and not letting good data be explained poorly through bad writing. It also covers writing micro-articles, determining significance, using active voice, nominalizations, and sentence structure.
THIS PRESENTATION REPRESENTS IN A NUTSHELL THE CORE OF RESEARCH MADE BETWEEN 1995 AND 2001 AT THE UNIVERSITY OF NIJMEGEN (NL) AND AT ENEA CASACCIA RESEARCH CENTRE (IT).
RNA-Seq Analysis of Blueberry Fruit Development and RipeningAnn Loraine
This document summarizes an RNA-Seq analysis of blueberry fruit development and ripening. Researchers sequenced RNA from five stages of fruit development to generate over 20 million reads per sample. Reads were aligned to the blueberry genome assembly to identify over 50,000 expressed genes and their expression profiles across stages. Analysis identified thousands of differentially expressed genes between stages and clusters of genes with similar expression patterns. Pathway analysis revealed metabolic pathways active during fruit development, including a potential new pathway for bixin biosynthesis with high expression during fruit maturation. Resources from the project include an online blueberry browser and gene expression data.
This document summarizes the key enzymatic and physiological changes that occur during fruit ripening, including enzymatic changes, changes in texture, respiration, and transpiration. It discusses how ripening is initiated by enzymes like pectinesterase, polygalacturonase, and cellulase, which cause softening by breaking down cell walls. Respiration increases during ripening, especially in climacteric fruits, while transpiration causes water loss. Studies on different fruits like guava, papaya, and banana are referenced to show how these changes have been observed and impact quality.
Bananas are one of the oldest tropical fruits cultivated by humans. India is the largest producer and exporter of bananas in the world. There are several factors that influence the maturity and post-harvest quality of bananas. Bananas are climacteric fruits that can be harvested mature-green and ripened off the plant, extending their post-harvest life. Proper harvesting, handling, storage and ripening conditions are required to maintain banana quality and prevent deterioration. The key factors affecting post-harvest quality include temperature, humidity, ethylene production and respiration rate.
RNAi – Mechanism and Its Application In Crop Improvementkundan Jadhao
This document summarizes an RNAi presentation on crop improvement using RNA interference. The 3-sentence summary is:
RNA interference (RNAi) is a process of post-transcriptional gene silencing mediated by small RNA molecules. The presentation described the RNAi pathway and various applications of RNAi technology in crop improvement, including increasing nutrient levels, developing virus and pest resistance, and reducing anti-nutritional compounds. Several case studies were provided that demonstrated how RNAi has been used to successfully modify traits in different crops like maize, cotton, coffee, and banana.
This document discusses fruit ripening with a focus on banana ripening. It defines fruit ripening as the process where fruits become edible by becoming sweeter, softer and less green. It classifies fruits as either climacteric, which continue ripening off the plant, or non-climacteric, which do not ripen further after harvesting. Bananas are used as an example of a climacteric fruit. The document outlines controlled ripening techniques used commercially, including regulating ethylene gas levels, temperature, humidity and air circulation to optimize ripening and extend shelf life. It provides details on ripening rooms and procedures used specifically for banana ripening.
Its about how fruit ripening occurs and how we can manipulate ripening process by using biotechnology to delay ripening and to reduce postharvest losses
The document summarizes key aspects of physiology related to fruit set, growth, drop, and ripening in vegetable crops. It discusses factors that influence fruit set like receptivity, growth relations, and parthenocarpy. It also describes stages of fruit growth including rates, mobilization of nutrients, role of seeds, and growth substances. The document then covers physiology of fruit drop and factors involved like auxins, abscissic acid, and ethylene. Finally, it summarizes important events during fruit ripening like softening, hydrolysis of storage materials, and changes to pigments and flavors.
SMi is proud to present its 6th conference on RNAi, miRNA and siRNA which shall tackle some of the most prominent issues that stand in the way of the successful harnessing of the vast potential that the process possesses. RNAi is still a new and exciting area of pharmaceutical development, however significant progress is required in certain areas, in achieving successful targeted delivery and tackling off targeting as two examples.
This conference will display some of the most promising results achieved; from structural determination through to specific therapeutic applications, clinical trial considerations and negotiating the regulatory minefield, attendees can be sure to expect an invaluable learning and networking experience.
This document discusses fruit development and factors that influence fruit size. It explains that fruits develop from ovaries and accessory tissues, and can have different structures depending on flower anatomy. Fruit development involves cell division, cell expansion, and ripening. The size of fruits is influenced by the number of cells formed in the division phase, the number of leaves per fruit providing photosynthates, competition between fruits for resources, and seed formation which stimulates growth. Horticulturists can increase fruit size by thinning fruits early in development to reduce competition during cell division.
This document defines epigenetics as heritable changes in gene expression that are not caused by changes in DNA sequence. It discusses genomic imprinting, where alleles from the father and mother are expressed differently. Genomic imprinting is explained by the parental conflict theory, which posits that genes have evolved conflicting interests in how much they provision offspring depending on whether they are inherited from the father or mother. Imprinting marks on DNA are established differently depending on the parent of origin and can be erased in germ line cells, but reestablished in offspring. Problems can occur if imprinting marks are defective or the wrong parental alleles are inherited.
Applications of genetic engineering techniques in agricultureB.Devadatha datha
This document discusses applications of genetic engineering techniques in agriculture. It begins by outlining reasons for genetically engineering plants, such as improving crops, using plants as bioreactors, and studying gene action. Various genetic engineering methods are then described, including Agrobacterium-mediated gene transfer. Applications like developing herbicide-resistant, insect-resistant, virus-resistant, and drought/cold-tolerant crops are covered. The document also discusses using genetic engineering for nutritional enhancement and production of edible vaccines. Potential risks like contamination and effects on non-target organisms are noted.
DNA methylation is an epigenetic mechanism that involves the addition of a methyl group to cytosine residues in DNA. It is catalyzed by DNA methyltransferase enzymes and plays a key role in gene expression and cellular differentiation. Aberrant DNA methylation, including both hypermethylation and hypomethylation, has been associated with cancer development by disrupting gene expression. Detection of DNA methylation patterns can provide insights into cancer biology and may have applications as a diagnostic tool.
RNAi is a powerful, conserved biological process through which the small, double-stranded RNAs specifically silence the expression of homologous genes, largely through degradation of their cognate mRNA.
THIS PRESENTATION REPRESENTS IN A NUTSHELL THE CORE OF RESEARCH MADE BETWEEN 1995 AND 2001 AT THE UNIVERSITY OF NIJMEGEN (NL) AND AT ENEA CASACCIA RESEARCH CENTRE (IT).
RNA-Seq Analysis of Blueberry Fruit Development and RipeningAnn Loraine
This document summarizes an RNA-Seq analysis of blueberry fruit development and ripening. Researchers sequenced RNA from five stages of fruit development to generate over 20 million reads per sample. Reads were aligned to the blueberry genome assembly to identify over 50,000 expressed genes and their expression profiles across stages. Analysis identified thousands of differentially expressed genes between stages and clusters of genes with similar expression patterns. Pathway analysis revealed metabolic pathways active during fruit development, including a potential new pathway for bixin biosynthesis with high expression during fruit maturation. Resources from the project include an online blueberry browser and gene expression data.
This document summarizes the key enzymatic and physiological changes that occur during fruit ripening, including enzymatic changes, changes in texture, respiration, and transpiration. It discusses how ripening is initiated by enzymes like pectinesterase, polygalacturonase, and cellulase, which cause softening by breaking down cell walls. Respiration increases during ripening, especially in climacteric fruits, while transpiration causes water loss. Studies on different fruits like guava, papaya, and banana are referenced to show how these changes have been observed and impact quality.
Bananas are one of the oldest tropical fruits cultivated by humans. India is the largest producer and exporter of bananas in the world. There are several factors that influence the maturity and post-harvest quality of bananas. Bananas are climacteric fruits that can be harvested mature-green and ripened off the plant, extending their post-harvest life. Proper harvesting, handling, storage and ripening conditions are required to maintain banana quality and prevent deterioration. The key factors affecting post-harvest quality include temperature, humidity, ethylene production and respiration rate.
RNAi – Mechanism and Its Application In Crop Improvementkundan Jadhao
This document summarizes an RNAi presentation on crop improvement using RNA interference. The 3-sentence summary is:
RNA interference (RNAi) is a process of post-transcriptional gene silencing mediated by small RNA molecules. The presentation described the RNAi pathway and various applications of RNAi technology in crop improvement, including increasing nutrient levels, developing virus and pest resistance, and reducing anti-nutritional compounds. Several case studies were provided that demonstrated how RNAi has been used to successfully modify traits in different crops like maize, cotton, coffee, and banana.
This document discusses fruit ripening with a focus on banana ripening. It defines fruit ripening as the process where fruits become edible by becoming sweeter, softer and less green. It classifies fruits as either climacteric, which continue ripening off the plant, or non-climacteric, which do not ripen further after harvesting. Bananas are used as an example of a climacteric fruit. The document outlines controlled ripening techniques used commercially, including regulating ethylene gas levels, temperature, humidity and air circulation to optimize ripening and extend shelf life. It provides details on ripening rooms and procedures used specifically for banana ripening.
Its about how fruit ripening occurs and how we can manipulate ripening process by using biotechnology to delay ripening and to reduce postharvest losses
The document summarizes key aspects of physiology related to fruit set, growth, drop, and ripening in vegetable crops. It discusses factors that influence fruit set like receptivity, growth relations, and parthenocarpy. It also describes stages of fruit growth including rates, mobilization of nutrients, role of seeds, and growth substances. The document then covers physiology of fruit drop and factors involved like auxins, abscissic acid, and ethylene. Finally, it summarizes important events during fruit ripening like softening, hydrolysis of storage materials, and changes to pigments and flavors.
SMi is proud to present its 6th conference on RNAi, miRNA and siRNA which shall tackle some of the most prominent issues that stand in the way of the successful harnessing of the vast potential that the process possesses. RNAi is still a new and exciting area of pharmaceutical development, however significant progress is required in certain areas, in achieving successful targeted delivery and tackling off targeting as two examples.
This conference will display some of the most promising results achieved; from structural determination through to specific therapeutic applications, clinical trial considerations and negotiating the regulatory minefield, attendees can be sure to expect an invaluable learning and networking experience.
This document discusses fruit development and factors that influence fruit size. It explains that fruits develop from ovaries and accessory tissues, and can have different structures depending on flower anatomy. Fruit development involves cell division, cell expansion, and ripening. The size of fruits is influenced by the number of cells formed in the division phase, the number of leaves per fruit providing photosynthates, competition between fruits for resources, and seed formation which stimulates growth. Horticulturists can increase fruit size by thinning fruits early in development to reduce competition during cell division.
This document defines epigenetics as heritable changes in gene expression that are not caused by changes in DNA sequence. It discusses genomic imprinting, where alleles from the father and mother are expressed differently. Genomic imprinting is explained by the parental conflict theory, which posits that genes have evolved conflicting interests in how much they provision offspring depending on whether they are inherited from the father or mother. Imprinting marks on DNA are established differently depending on the parent of origin and can be erased in germ line cells, but reestablished in offspring. Problems can occur if imprinting marks are defective or the wrong parental alleles are inherited.
Applications of genetic engineering techniques in agricultureB.Devadatha datha
This document discusses applications of genetic engineering techniques in agriculture. It begins by outlining reasons for genetically engineering plants, such as improving crops, using plants as bioreactors, and studying gene action. Various genetic engineering methods are then described, including Agrobacterium-mediated gene transfer. Applications like developing herbicide-resistant, insect-resistant, virus-resistant, and drought/cold-tolerant crops are covered. The document also discusses using genetic engineering for nutritional enhancement and production of edible vaccines. Potential risks like contamination and effects on non-target organisms are noted.
DNA methylation is an epigenetic mechanism that involves the addition of a methyl group to cytosine residues in DNA. It is catalyzed by DNA methyltransferase enzymes and plays a key role in gene expression and cellular differentiation. Aberrant DNA methylation, including both hypermethylation and hypomethylation, has been associated with cancer development by disrupting gene expression. Detection of DNA methylation patterns can provide insights into cancer biology and may have applications as a diagnostic tool.
RNAi is a powerful, conserved biological process through which the small, double-stranded RNAs specifically silence the expression of homologous genes, largely through degradation of their cognate mRNA.