The document discusses several topics in phylogenomics including:
1. Using phylogenomic approaches to study species evolution, lateral versus vertical gene transfer, gene function, gene and genome duplications, and genome rearrangements.
2. Examples of how comparative genomics can provide insights into these topics such as identifying horizontally transferred genes and organelle-derived genes in plant nuclear genomes.
3. The importance of evolutionary information for improving genome analysis and how genomic information can improve evolutionary reconstructions.
Talk on Phylogenomics for MBL Molecular Evolution Course 2004Jonathan Eisen
This document discusses phylogenomics and how analyzing genome sequences through an evolutionary lens can provide insights into how species evolve. It covers several topics: introducing phylogenomics and how evolutionary analysis is key to interpreting genomes; examples of phylogenomic studies of species evolution, uncultured organisms, and functional predictions; and the importance of increasing phylogenetic diversity in genome sequencing to better understand evolution. The document advocates for taking an evolutionary perspective in comparative genomic studies.
This document discusses methods for analyzing transgenic plants, including determining if a plant is transgenic and if transgenes are expressed. It describes established methods like PCR, Southern blots, and Northern blots. Southern blots are used to confirm transgene insertion into the genome by detecting fragments of different sizes after restriction enzyme digestion and gel electrophoresis. Northern blots detect RNA transcripts to confirm transgene expression. Proper experimental design and controls are important to avoid false positives and obtain conclusive evidence of stable transgene integration and expression.
This document discusses genetic markers and their use in plant breeding. It begins by defining genetic markers as locations on chromosomes that can be used as landmarks for genome analysis. It then provides examples of different types of markers, including morphological, biochemical, and molecular DNA-based markers. The bulk of the document focuses on DNA-based markers, describing different marker techniques, characteristics of good markers, and applications of markers such as gene tagging, mapping, and marker-assisted selection. It concludes by listing some DNA-based marker work being done at Indira Gandhi Krishi Vishwavidyalaya related to traits like drought tolerance and disease resistance.
A genetic marker is a gene or DNA sequence with a known location on a chromosome and associated with a particular gene or trait. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like mini & microsatellites.
This document summarizes transposon tagging as a method to identify genes. Transposon tagging involves inserting a transposon near a gene of interest, which then allows the gene to be identified based on its proximity to the transposon. The document discusses different types of transposons used for tagging in plants and animals. It describes approaches for both targeted and non-targeted tagging and methods for identifying the tagged gene, including RFLP analysis and inverse PCR. As an example, it summarizes how the Cf-9 gene conferring resistance to leaf mold in tomato was identified using Ds transposon tagging.
This document provides an overview of various gene transformation techniques, including both vector-mediated and direct methods. It discusses natural transformation mechanisms like conjugation and transduction, as well as artificial vector-mediated techniques like Agrobacterium-mediated transformation. Direct methods like microinjection, electroporation, particle bombardment, and chemical methods using PEG or calcium phosphate are also covered. The applications, advantages, and limitations of different techniques are summarized. Overall, the document serves as an informative introduction to the key gene transfer methods used in plant biotechnology.
Genetic markers can be used to track genes and chromosomes during genetic analysis. There are four main types of genetic markers: morphological, biochemical, cytological, and DNA markers. DNA markers are now widely used as they are not influenced by the environment and show high levels of polymorphism. Common types of DNA markers include restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), microsatellites, and single nucleotide polymorphisms (SNPs). DNA markers have advantages such as being easy to detect, exhibiting simple inheritance patterns, and showing minimal environmental influences. They have become powerful tools for applications like genetic mapping, diversity analysis, and gene tagging.
The document discusses genome sequencing in vegetable crops. It provides an overview of the history and different generations of sequencing including Sanger sequencing, second generation sequencing using platforms like Roche 454 and Illumina, and third generation sequencing. It then summarizes key vegetables whose genomes have been sequenced like potato, melon, cabbage, and discusses findings from their sequencing projects including genome size, number of predicted genes, and genes of interest identified.
Talk on Phylogenomics for MBL Molecular Evolution Course 2004Jonathan Eisen
This document discusses phylogenomics and how analyzing genome sequences through an evolutionary lens can provide insights into how species evolve. It covers several topics: introducing phylogenomics and how evolutionary analysis is key to interpreting genomes; examples of phylogenomic studies of species evolution, uncultured organisms, and functional predictions; and the importance of increasing phylogenetic diversity in genome sequencing to better understand evolution. The document advocates for taking an evolutionary perspective in comparative genomic studies.
This document discusses methods for analyzing transgenic plants, including determining if a plant is transgenic and if transgenes are expressed. It describes established methods like PCR, Southern blots, and Northern blots. Southern blots are used to confirm transgene insertion into the genome by detecting fragments of different sizes after restriction enzyme digestion and gel electrophoresis. Northern blots detect RNA transcripts to confirm transgene expression. Proper experimental design and controls are important to avoid false positives and obtain conclusive evidence of stable transgene integration and expression.
This document discusses genetic markers and their use in plant breeding. It begins by defining genetic markers as locations on chromosomes that can be used as landmarks for genome analysis. It then provides examples of different types of markers, including morphological, biochemical, and molecular DNA-based markers. The bulk of the document focuses on DNA-based markers, describing different marker techniques, characteristics of good markers, and applications of markers such as gene tagging, mapping, and marker-assisted selection. It concludes by listing some DNA-based marker work being done at Indira Gandhi Krishi Vishwavidyalaya related to traits like drought tolerance and disease resistance.
A genetic marker is a gene or DNA sequence with a known location on a chromosome and associated with a particular gene or trait. It can be described as a variation, which may arise due to mutation or alteration in the genomic loci that can be observed. A genetic marker may be a short DNA sequence, such as a sequence surrounding a single base-pair change (single nucleotide polymorphism, SNP), or a long one, like mini & microsatellites.
This document summarizes transposon tagging as a method to identify genes. Transposon tagging involves inserting a transposon near a gene of interest, which then allows the gene to be identified based on its proximity to the transposon. The document discusses different types of transposons used for tagging in plants and animals. It describes approaches for both targeted and non-targeted tagging and methods for identifying the tagged gene, including RFLP analysis and inverse PCR. As an example, it summarizes how the Cf-9 gene conferring resistance to leaf mold in tomato was identified using Ds transposon tagging.
This document provides an overview of various gene transformation techniques, including both vector-mediated and direct methods. It discusses natural transformation mechanisms like conjugation and transduction, as well as artificial vector-mediated techniques like Agrobacterium-mediated transformation. Direct methods like microinjection, electroporation, particle bombardment, and chemical methods using PEG or calcium phosphate are also covered. The applications, advantages, and limitations of different techniques are summarized. Overall, the document serves as an informative introduction to the key gene transfer methods used in plant biotechnology.
Genetic markers can be used to track genes and chromosomes during genetic analysis. There are four main types of genetic markers: morphological, biochemical, cytological, and DNA markers. DNA markers are now widely used as they are not influenced by the environment and show high levels of polymorphism. Common types of DNA markers include restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNA (RAPDs), microsatellites, and single nucleotide polymorphisms (SNPs). DNA markers have advantages such as being easy to detect, exhibiting simple inheritance patterns, and showing minimal environmental influences. They have become powerful tools for applications like genetic mapping, diversity analysis, and gene tagging.
The document discusses genome sequencing in vegetable crops. It provides an overview of the history and different generations of sequencing including Sanger sequencing, second generation sequencing using platforms like Roche 454 and Illumina, and third generation sequencing. It then summarizes key vegetables whose genomes have been sequenced like potato, melon, cabbage, and discusses findings from their sequencing projects including genome size, number of predicted genes, and genes of interest identified.
This document discusses the production of transgenic animals and plants. It describes three main methods for producing transgenic animals: DNA microinjection, retrovirus-mediated gene transfer, and embryonic stem cell-mediated gene transfer. It also discusses 11 methods for transforming plants, including Agrobacterium-mediated transformation, biolistic transformation, and floral dip transformation. Finally, it lists some beneficial traits that have been engineered in transgenic plants, such as stress tolerance, herbicide tolerance, and increased nutritional quality.
This document discusses various techniques used to analyze transgenic plants, including PCR, Southern blotting, Northern blotting, Western blotting, ELISA, and strip tests. PCR can detect the presence of a transgene but not copy number. Southern blotting determines transgene integration sites and copy number by detecting DNA fragments after restriction enzyme digestion. Northern blotting analyzes relative transgene expression at the mRNA level. Western blotting and ELISA detect and quantify transgene protein production. Strip tests provide a rapid, qualitative method to detect transgene proteins. Together, these techniques allow analysis of transgenic plants at the DNA, RNA, and protein levels.
Strategies to Remove Selectable Marker Genes from Transgenic PlantsKarthik P Bhat
This document discusses strategies for removing selectable marker genes (SMGs) from transgenic plants. It describes various methods used for plant transformation including co-transformation, which involves simultaneously transforming plants with the gene of interest and SMG located on different vectors. It then summarizes different approaches for removing the SMG after selection including genetic segregation, site-specific recombination, and transposition-based methods. The document provides examples of each type of SMG removal strategy that has been demonstrated successfully in transgenic plants.
Genomics is being widely applied in animal agriculture. It allows identification of genes associated with traits like disease resistance and production to select superior breeding animals. Techniques include cloning, genetic engineering of transgenic animals, and gene therapy. Genomic selection is revolutionizing livestock breeding by enabling early selection of breeding stock and improving genetic gains.
Genomics refers to the study of the entire genome of an organism. It deals with mapping genes on chromosomes and sequencing entire genomes. While work on genomics began with prokaryotes like bacteria, research has now been conducted on crop plants like rice and Arabidopsis thaliana. Genomics is an interdisciplinary field that uses tools from molecular biology, robotics, and computing to study genomes. It provides information on genome size, gene number, gene function, and evolution. Genomics has applications in crop improvement through gene mapping, marker-assisted selection, and transgenic breeding. However, genomic research also faces limitations due to high costs, technical challenges, and complexity of traits.
This document provides an overview of rice genomics. It discusses the history of genomics from the 1980s development of DNA markers and PCR, to major milestones like the sequencing of rice genomes in 2002. It describes the International Rice Genome Sequencing Project's clone-by-clone sequencing approach. The rice genome was found to contain over 37,000 genes and significant repetitive elements. Comparative genomics with other cereals revealed conserved synteny. The 3,000 Rice Genomes Project aims to sequence a diverse set of rice varieties to explore genetic diversity.
This document provides an overview of genetic engineering. It begins with definitions of key terms like genes, DNA, and genetically modified organisms. It then describes the basic 5-step process of genetic engineering: isolation of the desired gene, cutting with restriction enzymes, insertion into a vector, transformation of a host cell, and expression of the new gene. Examples are given of genetic engineering applications for creating plants resistant to herbicides and animals that produce human proteins. Potential risks discussed include effects on human health, biodiversity, and animal welfare. The document concludes by questioning if genetic engineering is ready for its consequences.
Introduction to Genetic engineering
Process:
Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology.
It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms.
New DNA is obtained by either isolating and copying the genetic material of interest using recombinant DNA methods or by artificially synthesising the DNA.
Gene knock out technology uses embryonic stem cells to introduce targeted mutations into the mouse genome, allowing the study of gene function. A targeting vector containing the mutated gene sequence flanked by homologous DNA is introduced into embryonic stem cells. Cells with the mutation incorporated via homologous recombination are identified and injected into blastocysts, generating chimeric mice. Breeding of these mice can produce strains lacking the gene of interest, enabling investigation into the effects of its absence. This technology was developed in the 1980s-1990s and its creators were awarded the 2007 Nobel Prize in Physiology or Medicine.
Diversity array technology (DArT) is a high-throughput marker system that does not require sequence information. DArT arrays have been developed for chickpea, pigeonpea, and groundnut comprising 15,360 clones each. DArT markers showed 35% and 9% polymorphism in chickpea and pigeonpea mapping populations, but are not cost-effective for detecting variation in cultivated germplasm. DArT may be useful for introgressing segments from wild species into elite varieties, as seen with introgressing resistance genes from C. platycarpus into pigeonpea. Next-generation sequencing has also been used to develop SSR markers for trait mapping in these
Gene transfer techniques can be direct or indirect. Direct techniques introduce foreign DNA into plant cells without a biological agent, using methods like microinjection, microprojectiles, protoplast fusion, electroporation, and polyethylene glycol treatment. Indirect gene transfer uses the bacterium Agrobacterium tumefaciens, which transfers DNA (T-DNA) from its tumor-inducing plasmid into the host plant genome, allowing genetic modification of plants. Techniques like bacterial transformation and transduction can also directly transfer genes between bacteria using viruses or naked DNA. Overall, a variety of methods have been developed to introduce foreign genes into organisms and achieve genetic modification.
A gene knockout is a genetic technique in which one of an organism's genes is made inoperative ("knocked out" of the organism). However, gene knockout can also refer to the gene that is knocked out or the organism that carries the gene knockout. Knockout organisms or simply knockouts are used to study gene function, usually by investigating the effect of gene loss. Researchers draw inferences from the difference between the knockout organism and normal individuals.
This document provides an overview of genomics and related fields. It discusses the historical discoveries that laid the foundations of genomics. It then defines key genomics terms and describes different areas of genomics research like comparative genomics, metagenomics, structural genomics, functional genomics, transcriptomics, proteomics and metabolomics. The document also discusses genome sequencing techniques, genome organization of different organisms like bacteria, plants and humans. It concludes with an overview of genome mapping methods.
This document discusses cisgenesis and intragenesis, which involve genetically modifying a crop plant using genes isolated from a crossable donor plant or from the same plant species, respectively. It defines cisgenic and intragenic plants and outlines their similarities and differences. It describes the prerequisites and various methods for constructing intragenic vectors and producing marker-free cisgenic/intragenic plants. The document presents several case studies demonstrating the development and evaluation of cisgenic plants with improved disease resistance. It discusses regulations around cisgenic/intragenic crops in different countries and potential benefits compared to transgenic and conventional breeding approaches.
This document discusses clean gene technology for developing transgenic plants without selectable marker genes. It presents 5 methods for producing marker-free transgenic plants: 1) co-transformation, 2) site-specific recombination-mediated marker deletion using the Cre/loxP system, 3) transposon-based marker methods, 4) intrachromosomal recombination, and 5) removal of chloroplast marker genes using homologous recombination. Each method is described briefly along with their advantages and limitations. The document concludes with a list of references on clean gene technology and selectable marker genes.
Gene transfer technology pharmacology biotechnology basic methods
Natural, physical, chemical methods of gene transfer.
Along with advantages and limitations, and applications.
This document outlines the structure and content of a three-part lecture series on the human genome taking place from October 12-16, 2014. Part I will provide an introduction and overview of genome sequencing technologies. Part II will discuss the human genome project and sequencing methods. Part III will cover genome assembly, annotation, outcomes including the number of genes and functional categories, and applications such as SNP analysis and genome-wide association studies. The overall goals are to understand principles of genome analysis and the impacts of the human genome project.
i have included terminology, types, methods, process, applications of trangenic technology.
all the pics are collected from different websites and some text books shown in reference. pictures and matter copyrights doesn't belong to me.
This document discusses various gene transfer methods. It defines gene transfer as the insertion of genetic material into a cell. There are natural methods like conjugation, transformation, and transduction that involve the transfer of genes between bacteria. There are also artificial physical, chemical, and electrical methods to transfer genes into cells, including microinjection, gene guns, calcium phosphate, liposomes, and electroporation. The document provides examples of how these various gene transfer methods can be used to insert genes into bacteria, plants, and animals.
The document discusses protein evolution, function, and human health. It provides an overview of why protein evolution matters for scientific curiosity, understanding disease, and more. It then covers major topics in protein evolution including processes like mutation and selection, as well as how protein function and structure impact evolution. Finally, it discusses practical applications like identifying disease-causing genes and mutations through an evolutionary lens.
Evolution of DNA repair genes, proteins and processesJonathan Eisen
This dissertation discusses the interface between evolution and DNA repair. It explores using comparative studies of repair genes and processes to study evolution. Differences in repair, such as mismatch repair, can drive evolution by affecting mutation rates and patterns. Evolutionary studies can benefit our understanding of repair mechanisms and gene families. The author developed "phylogenomics" to combine evolutionary reconstructions with genome analyses for improved inferences. Studies of RecA evolution, DNA turnover in E. coli, repair in Archaea, and adaptive mutation are presented.
This document discusses the production of transgenic animals and plants. It describes three main methods for producing transgenic animals: DNA microinjection, retrovirus-mediated gene transfer, and embryonic stem cell-mediated gene transfer. It also discusses 11 methods for transforming plants, including Agrobacterium-mediated transformation, biolistic transformation, and floral dip transformation. Finally, it lists some beneficial traits that have been engineered in transgenic plants, such as stress tolerance, herbicide tolerance, and increased nutritional quality.
This document discusses various techniques used to analyze transgenic plants, including PCR, Southern blotting, Northern blotting, Western blotting, ELISA, and strip tests. PCR can detect the presence of a transgene but not copy number. Southern blotting determines transgene integration sites and copy number by detecting DNA fragments after restriction enzyme digestion. Northern blotting analyzes relative transgene expression at the mRNA level. Western blotting and ELISA detect and quantify transgene protein production. Strip tests provide a rapid, qualitative method to detect transgene proteins. Together, these techniques allow analysis of transgenic plants at the DNA, RNA, and protein levels.
Strategies to Remove Selectable Marker Genes from Transgenic PlantsKarthik P Bhat
This document discusses strategies for removing selectable marker genes (SMGs) from transgenic plants. It describes various methods used for plant transformation including co-transformation, which involves simultaneously transforming plants with the gene of interest and SMG located on different vectors. It then summarizes different approaches for removing the SMG after selection including genetic segregation, site-specific recombination, and transposition-based methods. The document provides examples of each type of SMG removal strategy that has been demonstrated successfully in transgenic plants.
Genomics is being widely applied in animal agriculture. It allows identification of genes associated with traits like disease resistance and production to select superior breeding animals. Techniques include cloning, genetic engineering of transgenic animals, and gene therapy. Genomic selection is revolutionizing livestock breeding by enabling early selection of breeding stock and improving genetic gains.
Genomics refers to the study of the entire genome of an organism. It deals with mapping genes on chromosomes and sequencing entire genomes. While work on genomics began with prokaryotes like bacteria, research has now been conducted on crop plants like rice and Arabidopsis thaliana. Genomics is an interdisciplinary field that uses tools from molecular biology, robotics, and computing to study genomes. It provides information on genome size, gene number, gene function, and evolution. Genomics has applications in crop improvement through gene mapping, marker-assisted selection, and transgenic breeding. However, genomic research also faces limitations due to high costs, technical challenges, and complexity of traits.
This document provides an overview of rice genomics. It discusses the history of genomics from the 1980s development of DNA markers and PCR, to major milestones like the sequencing of rice genomes in 2002. It describes the International Rice Genome Sequencing Project's clone-by-clone sequencing approach. The rice genome was found to contain over 37,000 genes and significant repetitive elements. Comparative genomics with other cereals revealed conserved synteny. The 3,000 Rice Genomes Project aims to sequence a diverse set of rice varieties to explore genetic diversity.
This document provides an overview of genetic engineering. It begins with definitions of key terms like genes, DNA, and genetically modified organisms. It then describes the basic 5-step process of genetic engineering: isolation of the desired gene, cutting with restriction enzymes, insertion into a vector, transformation of a host cell, and expression of the new gene. Examples are given of genetic engineering applications for creating plants resistant to herbicides and animals that produce human proteins. Potential risks discussed include effects on human health, biodiversity, and animal welfare. The document concludes by questioning if genetic engineering is ready for its consequences.
Introduction to Genetic engineering
Process:
Genetic engineering, also called genetic modification or genetic manipulation, is the direct manipulation of an organism's genes using biotechnology.
It is a set of technologies used to change the genetic makeup of cells, including the transfer of genes within and across species boundaries to produce improved or novel organisms.
New DNA is obtained by either isolating and copying the genetic material of interest using recombinant DNA methods or by artificially synthesising the DNA.
Gene knock out technology uses embryonic stem cells to introduce targeted mutations into the mouse genome, allowing the study of gene function. A targeting vector containing the mutated gene sequence flanked by homologous DNA is introduced into embryonic stem cells. Cells with the mutation incorporated via homologous recombination are identified and injected into blastocysts, generating chimeric mice. Breeding of these mice can produce strains lacking the gene of interest, enabling investigation into the effects of its absence. This technology was developed in the 1980s-1990s and its creators were awarded the 2007 Nobel Prize in Physiology or Medicine.
Diversity array technology (DArT) is a high-throughput marker system that does not require sequence information. DArT arrays have been developed for chickpea, pigeonpea, and groundnut comprising 15,360 clones each. DArT markers showed 35% and 9% polymorphism in chickpea and pigeonpea mapping populations, but are not cost-effective for detecting variation in cultivated germplasm. DArT may be useful for introgressing segments from wild species into elite varieties, as seen with introgressing resistance genes from C. platycarpus into pigeonpea. Next-generation sequencing has also been used to develop SSR markers for trait mapping in these
Gene transfer techniques can be direct or indirect. Direct techniques introduce foreign DNA into plant cells without a biological agent, using methods like microinjection, microprojectiles, protoplast fusion, electroporation, and polyethylene glycol treatment. Indirect gene transfer uses the bacterium Agrobacterium tumefaciens, which transfers DNA (T-DNA) from its tumor-inducing plasmid into the host plant genome, allowing genetic modification of plants. Techniques like bacterial transformation and transduction can also directly transfer genes between bacteria using viruses or naked DNA. Overall, a variety of methods have been developed to introduce foreign genes into organisms and achieve genetic modification.
A gene knockout is a genetic technique in which one of an organism's genes is made inoperative ("knocked out" of the organism). However, gene knockout can also refer to the gene that is knocked out or the organism that carries the gene knockout. Knockout organisms or simply knockouts are used to study gene function, usually by investigating the effect of gene loss. Researchers draw inferences from the difference between the knockout organism and normal individuals.
This document provides an overview of genomics and related fields. It discusses the historical discoveries that laid the foundations of genomics. It then defines key genomics terms and describes different areas of genomics research like comparative genomics, metagenomics, structural genomics, functional genomics, transcriptomics, proteomics and metabolomics. The document also discusses genome sequencing techniques, genome organization of different organisms like bacteria, plants and humans. It concludes with an overview of genome mapping methods.
This document discusses cisgenesis and intragenesis, which involve genetically modifying a crop plant using genes isolated from a crossable donor plant or from the same plant species, respectively. It defines cisgenic and intragenic plants and outlines their similarities and differences. It describes the prerequisites and various methods for constructing intragenic vectors and producing marker-free cisgenic/intragenic plants. The document presents several case studies demonstrating the development and evaluation of cisgenic plants with improved disease resistance. It discusses regulations around cisgenic/intragenic crops in different countries and potential benefits compared to transgenic and conventional breeding approaches.
This document discusses clean gene technology for developing transgenic plants without selectable marker genes. It presents 5 methods for producing marker-free transgenic plants: 1) co-transformation, 2) site-specific recombination-mediated marker deletion using the Cre/loxP system, 3) transposon-based marker methods, 4) intrachromosomal recombination, and 5) removal of chloroplast marker genes using homologous recombination. Each method is described briefly along with their advantages and limitations. The document concludes with a list of references on clean gene technology and selectable marker genes.
Gene transfer technology pharmacology biotechnology basic methods
Natural, physical, chemical methods of gene transfer.
Along with advantages and limitations, and applications.
This document outlines the structure and content of a three-part lecture series on the human genome taking place from October 12-16, 2014. Part I will provide an introduction and overview of genome sequencing technologies. Part II will discuss the human genome project and sequencing methods. Part III will cover genome assembly, annotation, outcomes including the number of genes and functional categories, and applications such as SNP analysis and genome-wide association studies. The overall goals are to understand principles of genome analysis and the impacts of the human genome project.
i have included terminology, types, methods, process, applications of trangenic technology.
all the pics are collected from different websites and some text books shown in reference. pictures and matter copyrights doesn't belong to me.
This document discusses various gene transfer methods. It defines gene transfer as the insertion of genetic material into a cell. There are natural methods like conjugation, transformation, and transduction that involve the transfer of genes between bacteria. There are also artificial physical, chemical, and electrical methods to transfer genes into cells, including microinjection, gene guns, calcium phosphate, liposomes, and electroporation. The document provides examples of how these various gene transfer methods can be used to insert genes into bacteria, plants, and animals.
The document discusses protein evolution, function, and human health. It provides an overview of why protein evolution matters for scientific curiosity, understanding disease, and more. It then covers major topics in protein evolution including processes like mutation and selection, as well as how protein function and structure impact evolution. Finally, it discusses practical applications like identifying disease-causing genes and mutations through an evolutionary lens.
Evolution of DNA repair genes, proteins and processesJonathan Eisen
This dissertation discusses the interface between evolution and DNA repair. It explores using comparative studies of repair genes and processes to study evolution. Differences in repair, such as mismatch repair, can drive evolution by affecting mutation rates and patterns. Evolutionary studies can benefit our understanding of repair mechanisms and gene families. The author developed "phylogenomics" to combine evolutionary reconstructions with genome analyses for improved inferences. Studies of RecA evolution, DNA turnover in E. coli, repair in Archaea, and adaptive mutation are presented.
1) The document questions the principles of evolution and argues that life is too complex to have originated through natural processes alone.
2) It argues that the first cell could not have formed by chance and notes that the origin of protein and DNA is not explained by evolution.
3) The document also argues against common mechanisms of evolution like natural selection and mutation, noting a lack of transitional fossils between major animal groups.
All living things share DNA as their genetic code, which contains the instructions that determine an organism's characteristics. DNA evidence shows that all life on Earth evolved from a common ancestor, as organisms with more similar DNA are more closely related evolutionarily. Mutations in DNA over time led to the diversity of life we see today. Comparative anatomy, embryology, fossils, and DNA/protein evidence all support the theory of evolution through common descent.
Globulin proteins include hemoglobin, which transports oxygen in the blood and consists of eight alpha helices. Immunoglobulins are another type of globulin protein that function in the immune system, including five classes: IgA, IgD, IgE, IgG, and IgM. IgM is the first antibody produced during an initial immune response and forms pentamers to activate the complement system. The different immunoglobulin classes are believed to have evolved from a common ancestral gene through several gene duplication and divergence events.
Phylogenetic trees are branching diagrams that show the evolutionary relationships among various biological species based on similarities and differences in their physical or genetic characteristics. Each node represents the inferred most recent common ancestor of the descendants. Phylogenetic trees are constructed using character-based or distance-based methods and can be used to understand human and animal origins, molecular evolution processes, and the spread of disease.
This document provides an overview of key concepts from Chapter 21 of Campbell Biology about genomes and their evolution. It discusses the stages of genome sequencing, including genetic mapping, physical mapping, and DNA sequencing. It also describes how new sequencing techniques like whole-genome shotgun sequencing have accelerated the process. Bioinformatics tools are now used to analyze whole genomes and understand gene functions on a systems level. Comparisons of complete genome sequences from different organisms reveal variation in genome size, number of genes, and amount of noncoding DNA between domains of life.
The document summarizes key concepts about how genetic information flows from DNA to protein. It discusses how genes specify proteins through transcription and translation. Transcription involves RNA polymerase making an RNA copy of a gene. This RNA then undergoes processing in eukaryotes before being translated into a protein by ribosomes. The genetic code was discovered to be a triplet code of nucleotides that specifies which amino acid will be added during translation.
This document discusses protein engineering through directed evolution. It explains that directed evolution involves randomly recombining genes from protein libraries and screening mutant proteins for improved functions. This leaves beneficial changes up to chance but generates diversity. Rational design is also used to map important protein interactions to guide evolution. The document provides an example of using directed evolution to modify a cytochrome P450 enzyme to more efficiently convert alkanes to alcohols over multiple generations. However, it notes that expressing evolved proteins in vivo and requiring expensive cofactors limit the commercial potential of this approach.
Here is an analysis of variations in a red beetle population across three situations:
Situation 1 (Original population): The population consists of mostly red beetles, with a small percentage of black beetles. The red coloration provides better camouflage in their current environment.
Situation 2 (Environment change): The environment darkens due to increased vegetation/debris. Now black beetles have better camouflage than red beetles. Over time, the percentage of black beetles in the population will increase relative to red beetles, as black beetles survive and reproduce at a higher rate.
Situation 3 (New environment): The environment changes again, this time becoming lighter in color (e.g
Keynote talk at "Society for General Microbiology" meeting in March, 2001 by ...Jonathan Eisen
This document discusses genome sequencing and analysis from The Institute for Genomic Research (TIGR). It provides an overview of genome projects, what has been learned about evolution from genomes, and TIGR's role. Key points include that genome projects have provided insights into evolutionary processes like gene loss, duplication, rearrangements, and transfer. TIGR conducts microbial and eukaryotic genome sequencing and analysis to further evolutionary understanding.
Talk on Microbial Phylogenomics at the Society for General Microbiology meeti...Jonathan Eisen
This document discusses genome sequencing and analysis. It provides an overview of genome projects, what has been learned about evolution from genome sequencing, and themes of completeness and relatedness. It also discusses the Institute for Genomic Research, whole genome shotgun sequencing, general steps in genome analysis, and progress in microbial genome sequencing. Key findings on evolution from complete genomes include evidence of gene loss, duplication, genome rearrangements, and horizontal gene transfer.
"Phylogenomics: Combining Evolutionary Reconstructions and Genome Analysis in...Jonathan Eisen
Talk by Jonathan Eisen given in December 2000 as guest seminar at the University of Maryland. Title; "Phylogenomics: Combining Evolutionary Reconstructions and Genome Analysis into a Single Composite Approach"
Phylogenomics talk in 2000 at University of Maryland by J. EisenJonathan Eisen
This document discusses phylogenomics, which combines evolutionary reconstructions and genome analysis into a single approach. It provides examples of how phylogenomic analysis can be used for functional predictions by examining the MutS family of proteins. A BLAST search of the H. pylori "MutS" protein initially suggested it was most similar to MutS2 from Syn. sp. A phylogenetic tree of the MutS family revealed that H. pylori MutS fell into a distinct subfamily, suggesting it may have a divergent function compared to other known MutS proteins.
This document discusses various plant transformation systems. It describes direct transformation techniques like microinjection, electroporation, silicon carbide-mediated and gene gun/biolistic transformation. It also discusses indirect transformation techniques like Agrobacterium tumefaciens-mediated and virus-mediated gene transfer. Agrobacterium tumefaciens is able to transfer T-DNA from its Ti plasmid into the plant genome. Viral vectors like caulimoviruses and geminiviruses are also used for plant transformation. The document further explains in planta transformation techniques like meristem transformation and floral dip method. It provides examples of transgenic crops developed using these techniques.
Genomics and its application in crop improvementKhemlata20
meaning ,definition of genome ,genomics ,tools of genomics ,what is genome sequencing ,methods of genome sequencingand genome mapping ,advantage of genomics over traditional breeding program, examples of some crops whose genome has been sequenced, important points about genomics, work in the field of genomics ,applications of genomics .classification of genomics .different Omics in genomics like Proteomics ,Transcriptomics ,Metabolomics ,Need of genome sequencing
Improving cold storage and processing traits in potatoSarbesh D. Dangol
This document summarizes a research article that used targeted gene knockout to improve cold storage and processing traits in potato. The researchers used TALENs to generate mutations in the vacuolar invertase (VInv) gene in potato, which is responsible for accumulating reducing sugars during cold storage. This leads to cold-induced sweetening and the formation of carcinogenic acrylamide during processing. By knocking out the VInv gene in potato varieties Ranger Russet and others, the researchers found reduced reducing sugar levels and less browning and acrylamide formation during processing after cold storage. The targeted gene editing approach was more efficient than previous methods and could help improve potato varieties for storage and processing without introducing foreign DNA.
To achieve genetic transformation in plants, we need the construction of a vector (genetic vehicle) which transports the genes of interest, flanked by the necessary controlling sequences i.e. promoter and terminator, and deliver the genes into the host plant.
This document discusses allele mining as a technique for improving crops. It defines allele mining as identifying allelic variation within genetic resources collections to find superior alleles. There are two main approaches - TILLING based allele mining which uses mutagenized populations and enzymatic cleavage to find mutations, and sequencing-based allele mining which uses PCR and sequencing to identify natural variation. Both have benefits and limitations. Applications of allele mining include finding alleles for resistance, abiotic stress tolerance, and improved yield and quality. Overall, allele mining is a promising approach for utilizing genetic resources to discover variants that can aid crop breeding.
Talk by Jonathan Eisen for GSAC2000 on "Phylogenomics"Jonathan Eisen
This document discusses phylogenomics, which combines evolutionary reconstructions and genome analysis into a single composite approach. It provides examples of how phylogenomics can be used to infer functional predictions, identify gene duplications, and compare closely related genomes. The document outlines the key components of a phylogenomic analysis, including constructing gene and species trees, analyzing patterns of presence/absence and evolutionary distribution of genes, and making functional predictions based on the integrated analysis.
Genomics is the study of genomes and includes determining entire DNA sequences, genetic mapping, and studying intragenomic phenomena. It allows determining an ideal genotype. Genomics and bioinformatics provide benefits like improved crop productivity, stress tolerance, and nutritional quality. Proteomics studies proteins in cells. Bioinformatics handles large genomic and proteomic data using algorithms. Structural genomics constructs sequence data and maps genes. Functional genomics studies gene function. Comparative genomics compares sequences to find relationships.
A new era of genomics for plant science research has opened due the complete genome sequencing projects of Arabidopsis thaliana and rice. The sequence information available in public database has highlighted the need to develop genome scale reverse genetic strategies for functional analysis (Till et al., 2003). As most of the phenotypes are obscure, the forward genetics can hardly meet the demand of a high throughput and large-scale survey of gene functions. Targeting Induced Local Lesions in Genome TILLING is a general reverse genetic technique that combines chemical mutagenesis with PCR based screening to identity point mutations in regions of interest (McCallum et al., 2000). This strategy works with a mismatch-specific endonuclease to detect induced or natural DNA polymorphisms in genes of interest. A newly developed general reverse genetic strategy helps to locate an allelic series of induced point mutations in genes of interest. It allows the rapid and inexpensive detection of induced point mutations in populations of physically or chemically mutagenized individuals. To create an induced population with the use of physical/chemical mutagens is the first prerequisite for TILLING approach. Most of the plant species are compatible with this technique due to their self-fertilized nature and the seeds produced by these plants can be stored for long periods of time (Borevitz et al., 2003). The seeds are treated with mutagens and raised to harvest M1 plants, which are consequently, self-fertilized to raise the M2 population. DNA extracted from M2 plants is used in mutational screening (Colbert et al., 2001). To avoid mixing of the same mutation only one M2 plant from each M1 is used for DNA extraction (Till et al., 2007). The M3 seeds produce by selfing the M2 progeny can be well preserved for long term storage. Ethyl methane sulfonate (EMS) has been extensively used as a chemical mutagen in TILLING studies in plants to generate mutant populations, although other mutagens can be effective. EMS produces transitional mutations (G/C, A/T) by alkylating G residues which pairs with T instead of the conservative base pairing with C (Nagy et al., 2003). It is a constructive approach for users to attempt a range of chemical mutagens to assess the lethality and sterility on germinal tissue before creating large mutant populations.
Methods of Gene Transfer document discusses various methods of transferring genes into plants to create transgenic plants. It describes two main categories of gene transfer methods - physical and biological. Physical methods include microinjection, biolistics (gene gun), electroporation, and particle bombardment. Biological methods include Agrobacterium-mediated transformation, which involves using the bacteria Agrobacterium tumefaciens to transfer DNA into plant cells. The document also discusses transformation cassettes, selection of transgenic plants, analysis of transgenic plants, and some examples of commercially important transgenic crops like golden rice and Roundup Ready corn.
Genomics refers to the study of the structure and function of an organism's entire genome. It deals with mapping genes on chromosomes and sequencing genes. Genomics uses tools from molecular biology, robotics, and computing to analyze large amounts of genomic data. The term was first used in 1986 to describe mapping, sequencing, and characterizing genomes. Genome mapping has been completed for many prokaryotes and eukaryotes, including bacteria, yeast, fruit flies, humans, and some crop plants like rice and Arabidopsis thaliana. Genomics is useful for crop improvement as it allows determining genome size and gene number, mapping and sequencing genes, tracing crop evolution, and identifying DNA markers for applications like marker-assisted selection and transgenic
1. Forward genetics begins with the identification of an organism with an interesting mutant phenotype and aims to discover the function of genes defective in that mutant. It involves mutagenesis, screening for phenotypes of interest, genetic analysis, and chromosome walking to identify the mutated gene.
2. Reverse genetics starts with a known gene and determines the gene's function by modulating its activity through techniques like virus-induced gene silencing, RNA interference, TILLING, and gene deletion and observing resulting phenotypes in the organism.
3. Both forward and reverse genetics are aided by high-throughput approaches like insertional mutagenesis, which allows for rapid screening of large mutant collections to efficiently link phenotypes to genes.
This document discusses Arabidopsis thaliana and its use in molecular biology research. Some key points:
- A. thaliana is well-suited for genetic research due to its small size, short life cycle, and large seed production. It was the first plant genome sequenced.
- Its genome of about 135 Mbp is among the smallest for higher plants. It contains 5 chromosomes useful for genetic mapping and sequencing.
- The document discusses forward and reverse genetics techniques used to study gene function in A. thaliana such as mutagenesis, screening mutants, positional cloning, and RNA interference. It provides examples of how these approaches have furthered understanding of plant genes and processes.
The document summarizes research on temperate bacteriophages that infect mycobacteria. It describes isolating two new phages, Hetaeria and QuinnKiro, and characterizing their genomes, which were found to contain stoperator sequences near genes related to lysis. Mass spectrometry analysis of infected cells identified over half of predicted proteins in Hetaeria, revealing functions and modifications. Future work aims to compare proteomics of lytic and temperate phages.
TIGR "Tree of Life" Project Slides (from 2004)Jonathan Eisen
This document describes the TIGR Tree of Life project which aims to sequence genomes from uncultured bacterial phyla to help resolve relationships among major bacterial lineages and advance the study of uncultured microbes. The project involves sequencing genomes from underrepresented phyla to build a more comprehensive bacterial tree of life and enable studies of the biology and ecology of uncultured bacteria through genomics. Genome sequencing is underway for several understudied phyla and the data will be used to anchor phylogenetic analysis of environmental samples to link bacterial identities to potential functions.
Similar to Jonathan Eisen lecture for MBL Molecular Evolution Course 2003 (20)
Innovations in Sequencing & Bioinformatics
Talk for
Healthy Central Valley Together Research Workshop
Jonathan A. Eisen University of California, Davis
January 31, 2024 linktr.ee/jonathaneisen
Talk by Jonathan Eisen for LAMG2022 meetingJonathan Eisen
The document discusses the history of the Lake Arrowhead Microbial Genomes (LAMG) conference. It reveals that LAMG2020 was cancelled due to a secret plan by organizers who formed an "anti-karyote society" that hates eukaryotes. The meeting was to be renamed the "Big, Large, Enormous" meeting of the Lake Arrowhead Big Large Enormous Anti-Karyote Society. The document also hints that several past LAMG speakers have made cryptic comments indicating involvement in a conspiracy surrounding the conference.
Thoughts on UC Davis' COVID Current ActionsJonathan Eisen
Slides I used for a presentation to Chancellor May's leadership council about the current state of UC Davis' response to COVID and how it could be improved
Phylogenetic and Phylogenomic Approaches to the Study of Microbes and Microbi...Jonathan Eisen
The document discusses Jonathan Eisen's work as a microbiology professor at UC Davis. It provides an overview of his research topics, which include microbial phylogenomics and evolvability, phylogenetic methods and tools, and using phylogenomics to study microbial communities and interactions between microbes and hosts under stress. The document also acknowledges collaborators and funding sources for Eisen's research over the years.
This document summarizes a class on detecting, quantifying, and tracking variations of SARS-CoV-2 RNA from COVID-19 samples. It discusses using quantitative RT-PCR (qRT-PCR) to detect and measure viral RNA levels in samples. Sequencing is used to identify variations in the viral genome over time, and online tools like Nextstrain allow viewing the evolution and global transmission of variants. Genotyping assays are also described that can rapidly screen samples for known single nucleotide variations during PCR.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 8 - COVID RNA DetectionJonathan Eisen
This document summarizes a class on SARS-CoV-2 RNA detection, quantification, and variation. It discusses how qRT-PCR is used to detect and quantify the virus by amplifying and detecting viral RNA. It also covers sequencing to identify variants, how variants evolve over time, and genotyping assays that can screen samples for known single nucleotide variations. Nextstrain and other online tools are presented that use sequencing data to analyze viral phylogenies, track variant distributions globally, and visualize genetic variations across the SARS-CoV-2 genome.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms for those who already suffer from conditions like depression and anxiety.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Winter2020 Class 5 - COVID VaccinesJonathan Eisen
The document discusses a class on COVID-19 vaccines. It covers topics like vaccine development, current candidates, delivery challenges, and comparisons between vaccines. Moderna and Pfizer mRNA vaccines are highlighted as being similar but having some differences in mRNA region, nanoparticle structure/synthesis, dosage amount, and storage temperature requirements. Other vaccines discussed include Novavax using spike protein nanoparticles, and AstraZeneca and Johnson & Johnson using DNA for spike protein delivered by a modified virus.
EVE198 Winter2020 Class 9 - COVID TransmissionJonathan Eisen
This document discusses modes of SARS-CoV-2 transmission including droplets, aerosols, and surfaces. It emphasizes that surfaces are not as big a risk as initially thought. It provides guidance on limiting transmission from different modes such as distancing, masks, washing hands, cleaning surfaces, and improving ventilation. The focus in 2021 is on droplets and aerosols rather than surfaces.
EVE198 Fall2020 "Covid Mass Testing" Class 8 VaccinesJonathan Eisen
This document discusses a class on vaccines for COVID-19. It covers topics like vaccine development, current candidate vaccines, challenges with vaccine distribution, and how vaccines are being assessed for safety, effectiveness, costs and production feasibility. Over 100 vaccine candidates are in development using platforms like DNA, RNA, viral vectors and inactivated viruses. Efforts like Operation Warp Speed are coordinating development of nucleic acid, viral vector and protein subunit vaccines. Distribution challenges include vaccine production, storage and logistics, number of doses required, and overcoming vaccine nationalism and hesitancy.
EVE198 Fall2020 "Covid Mass Testing" Class 2: Viruses, COIVD and TestingJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
EVE198 Fall2020 "Covid Mass Testing" Class 1 IntroductionJonathan Eisen
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
BREEDING METHODS FOR DISEASE RESISTANCE.pptxRASHMI M G
Plant breeding for disease resistance is a strategy to reduce crop losses caused by disease. Plants have an innate immune system that allows them to recognize pathogens and provide resistance. However, breeding for long-lasting resistance often involves combining multiple resistance genes
The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptxMAGOTI ERNEST
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
Phenomics assisted breeding in crop improvementIshaGoswami9
As the population is increasing and will reach about 9 billion upto 2050. Also due to climate change, it is difficult to meet the food requirement of such a large population. Facing the challenges presented by resource shortages, climate
change, and increasing global population, crop yield and quality need to be improved in a sustainable way over the coming decades. Genetic improvement by breeding is the best way to increase crop productivity. With the rapid progression of functional
genomics, an increasing number of crop genomes have been sequenced and dozens of genes influencing key agronomic traits have been identified. However, current genome sequence information has not been adequately exploited for understanding
the complex characteristics of multiple gene, owing to a lack of crop phenotypic data. Efficient, automatic, and accurate technologies and platforms that can capture phenotypic data that can
be linked to genomics information for crop improvement at all growth stages have become as important as genotyping. Thus,
high-throughput phenotyping has become the major bottleneck restricting crop breeding. Plant phenomics has been defined as the high-throughput, accurate acquisition and analysis of multi-dimensional phenotypes
during crop growing stages at the organism level, including the cell, tissue, organ, individual plant, plot, and field levels. With the rapid development of novel sensors, imaging technology,
and analysis methods, numerous infrastructure platforms have been developed for phenotyping.
ESR spectroscopy in liquid food and beverages.pptxPRIYANKA PATEL
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...AbdullaAlAsif1
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
Or: Beyond linear.
Abstract: Equivariant neural networks are neural networks that incorporate symmetries. The nonlinear activation functions in these networks result in interesting nonlinear equivariant maps between simple representations, and motivate the key player of this talk: piecewise linear representation theory.
Disclaimer: No one is perfect, so please mind that there might be mistakes and typos.
dtubbenhauer@gmail.com
Corrected slides: dtubbenhauer.com/talks.html
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/
Nucleophilic Addition of carbonyl compounds.pptxSSR02
Nucleophilic addition is the most important reaction of carbonyls. Not just aldehydes and ketones, but also carboxylic acid derivatives in general.
Carbonyls undergo addition reactions with a large range of nucleophiles.
Comparing the relative basicity of the nucleophile and the product is extremely helpful in determining how reversible the addition reaction is. Reactions with Grignards and hydrides are irreversible. Reactions with weak bases like halides and carboxylates generally don’t happen.
Electronic effects (inductive effects, electron donation) have a large impact on reactivity.
Large groups adjacent to the carbonyl will slow the rate of reaction.
Neutral nucleophiles can also add to carbonyls, although their additions are generally slower and more reversible. Acid catalysis is sometimes employed to increase the rate of addition.
3. TIGRTIGR
Topics of Discussion
• Introduction to genome sequencing and
analysis
• Need for “phylogenomic” approaches
• Phylogenomic examples
– Species evolution
– Lateral vs. vertical evolution
– Gene function
– Gene duplications
– Genome rearrangements
4. TIGRTIGR
The Institute for Genomic Research
(TIGR)
• A not for profit institution, staff ~350
• Funded primarily by government
grants
• Departments:
– Research Departments
– Bioinformatics
– Sequencing Core
8. TIGRTIGR
General Steps in Analysis of
Complete Genomes
• Identification/prediction of genes
• Characterization of gene features
• Characterization of genome features
• Prediction of gene function
• Prediction of pathways
• Integration with known biological data
9. TIGRTIGR
Comparative Genomics
• Comparison of genomes between species
• Identify differences
– SNPs
– Indels
– Rearrangements
– Presence/absence of genes, pathways, features
• Correlating with phenotypic differences
• Can be used to improve on every step in genome
analysis
14. TIGRTIGR
Evolution and Genomics Overlap
• Genome sequences contain a record of the
evolution of a species and all its genes
• Evolutionary analysis is the key to
interpreting genome sequences and making
the most use out of them
15. TIGRTIGR
Phylogenomics?
Evolutionary information improves genome analysis
-Classification of multigene families
-Predicting functions
-Origins of genes and pathways
Genomics information improves evolutionary
reconstructions
-More sequences of genes
-Unbiased sampling
-Presence/absence needed to infer certain events
Feedback loop between two types of analysis
TIGRTIGR
17. TIGRTIGR
Why Completeness is Important
• Improves characterization of genome features
– Gene order, replication origins
• Better comparative genomics
– Genome duplications, inversions
• Determination of presence and absence of particular genes and
features is less subjective
• Missing sequence might be important (e.g., centromere)
• Allows researchers to focus on biology not sequencing
• Facilitates large scale correlation studies
• Controls for contamination
18. TIGRTIGR
Uses of Phylogenomics
• Species evolution and systematics
• Lateral versus vertical evolution
• Gene function
• Gene and genome duplications
• Genome rearrangements
20. TIGRTIGR
Species EvolutionI I:
Major Evolutionary Transitions
• Analysis of S. pombe genome (Wood et al 2002)
• Compared the genomes of eukaryotes to those of
prokaryotes
• Asked: “Are there genes in all eukaryotes with no obvious
homologs in any prokaryote?”
• Found ~200 genes which included many with know major
roles in “eukaryotic” features like the cytoskeleton and
chromatin as well as many with no known function
22. TIGRTIGR
Evolutionary Transitions II:
Single- vs. Multi-Cellularity
• Analysis of S. pombe genome (Wood et al. 2002)
• Compared multi-cellular vs. single-cellular species
• Asked “Are there genes in all multi-cellular and not in any
single-cellular?”
• Found only 3
• Concluded that the multicellularity was likely the result of
gene regulatory processes
24. TIGRTIGR
Species Evolution III:
Uncultured Microbes
• Vast majority of
microbes have never
been cultured
• Usually studied
indirectly by cloning
rRNA genes and using
position within rRNA
tree to predict biology
• These predictions are
frequently inaccurate
25. TIGRTIGR
Genomics does not require initial
culturing step.
• Isolate, by filtration, all bacteria in a water sample
• Extract total DNA in very large pieces
• Clone those pieces as BACs into E.coli to get enough.
• Sequence the BACs like a bacterial genome.
Natural
Water
Filter
concentrate
Extract
DNA
Clone
Into
BACs
Sequence
Gene
List
27. TIGRTIGR
Using a rRNA anchor
allowed the
identification of a new
form of phototrophy:
Proteorhodopsin
Beja et al. 2000
28. TIGRTIGR
Uses of Phylogenomics
• Species evolution and systematics
• Lateral versus vertical evolution
• Gene function
• Gene and genome duplications
• Genome rearrangements
30. TIGRTIGR
Examples of Horizontal
Transfers
• Antibiotic resistance genes
• Insertion sequences
• Agrobacterium Ti plasmid
• Toxin degradation genes on plasmids
• Virus and phage gene acquisition and
transfer
• Organelle to nucleus transfers
31. TIGRTIGR
Why Gene Transfers Are Useful to Identify
• Laterally transferred genes frequently involved in
environmental adaptations and/or pathogenicity
• Identification of vectors of gene transfer (e.g.,
transposons, integrons, phage)
• Identify species associations in the environment
(e.g., Thermotoga and Archaea, Nelson et al.)
• Identify organelle derived genomes in eukaryotic
genomes
33. TIGRTIGR
• Claim
– “Hundreds of human genes appear likely to have resulted from
horizontal transfer from bacteria at some point in the vertebrate
lineage.”
• Evidence
– Genes match bacteria but not non-vertebrate eukaryotes
– Or genes have stronger match to bacteria than to non-vertebrates
38. TIGRTIGR
Number of pBVTs Depends
on # of Genomes Analyzed
1 2 3 4 5 Other
0
200
400
600
800
1000
1200
1400
1600
1800
Number of protein sets
Fruit fly
C. elegans
Arabidopsis
Yeast
Parasites
Salzberg et al. 2001
44. TIGRTIGR
Mitochondrial Genome
Integration into A. thaliana chrII
3.2E+063.3E+063.4E+063.5E+063.6E+06D’1 A. thaliana
Mitochondrial
Alternative
Genome
Possible
Insertion
Point
3 D’1A’3C1B3B.C.D.Chromosome II1E+052E+053E+054E+05Alternative Mitochondrial Form03CBA’
45. TIGRTIGR
A. thaliana Nuclear Proteins:
Best Matches to Complete Genomes
0
1000
2000
3000
4000
BestMatches
CHLTE
PORGI
BACSU
MCYTU
BBUR
TREPA
CHLPN
ECOLI
NEIME
RICPR
CAUCR
HELPY
SYNSP
AQUAE
DEIRA
THEMA
AERPE
ARCFU
METJA
METTH
PYRAB
CELEG
YEAST
DROME
B A E
49. TIGRTIGR
A. thaliana T1E2.8 is a
Chloroplast Derived HSP60ARATH -T1E2.8**********ECOLHAEINVIBCHVIBCHRICPRYEASTCHLPNCHLTRAQUAECAMJEHELPYBBURTREPATHEMABACSUDEIRAMCYTUMCYTUSYNSPSYNSPODONT CPSTMYCGEMYCPNCHLPNCHLTRCHLPNCHLTRARCFUARCFUMETJAPYRHOMETTHMETTHYEASTYEASTYEASTYEASTCELEGYEASTYEASTYEASTCELEGYEASTYEASTCELEGYEASTCELEGCELEG
EukaryaArchaeaBacteriaCyano/Cpst
50. TIGRTIGR
Uses of Phylogenomics
• Species evolution and systematics
• Lateral versus vertical evolution
• Gene function
• Gene and genome duplications
• Genome rearrangements
51. TIGRTIGR
Predicting Function
• Identification of motifs
– Short regions of sequence similarity that are indicative of
general activity
– e.g., ATP binding
• Homology/similarity based methods
– Gene sequence is searched against a databases of other
sequences
– If significant similar genes are found, their functional
information is used
• Problem
– Genes frequently have similarity to hundreds of motifs
and multiple genes, not all with the same function
TIGRTIGR
53. TIGRTIGR
Blast Search of H. pylori “MutS”
Score E
Sequences producing significant alignments: (bits) Value
sp|P73625|MUTS_SYNY3 DNA MISMATCH REPAIR PROTEIN 117 3e-25
sp|P74926|MUTS_THEMA DNA MISMATCH REPAIR PROTEIN 69 1e-10
sp|P44834|MUTS_HAEIN DNA MISMATCH REPAIR PROTEIN 64 3e-09
sp|P10339|MUTS_SALTY DNA MISMATCH REPAIR PROTEIN 62 2e-08
sp|O66652|MUTS_AQUAE DNA MISMATCH REPAIR PROTEIN 57 4e-07
sp|P23909|MUTS_ECOLI DNA MISMATCH REPAIR PROTEIN 57 4e-07
• Blast search pulls up Syn. sp MutS#2 with
much higher p value than other MutS
homologs
55. TIGRTIGR
H. pylori and MutS
• Prior to this genome, all species that
encoded a MutS homolog also encoded
a MutL homolog
• Experimental studies have shown
MutS and MutL always work together
in mismatch repair
• Problem: what do we conclude about
H. pylori mismatch repair
58. TIGRTIGR
Phylogenetic Tree of MutS Family
Aquae Trepa
Fly
Xenla
Rat
Mouse
Human
Yeast
Neucr
Arath
Borbu
Strpy
Bacsu
Synsp
Ecoli
Neigo
Thema
TheaqDeira
Chltr
Spombe
Yeast
Yeast
Spombe
Mouse
Human
Arath
Yeast
Human
Mouse
Arath
StrpyBacsu
Celeg
Human
Yeast
MetthBorbu
Aquae
Synsp
Deira Helpy
mSaco
Yeast
Celeg
Human
66. TIGRTIGR
Evolutionary
Method
PHYLOGENENETIC PREDICTION OF GENE FUNCTIONIDENTIFY HOMOLOGSOVERLAY KNOWN
FUNCTIONS ONTO TREE
INFER LIKELY FUNCTION
OF GENE(S) OF INTEREST
1234563531A2A3A1B2B3B2A1B1A3A1B2B3BALIGN SEQUENCESCALCULATE GENE TREE1246CHOOSE GENE(S) OF INTEREST2A2A53Species 3Species 1Species 211222311A3A1A2A3A1A2A3A464564562B3B1B2B3B1B2B3B ACTUAL EVOLUTION
(ASSUMED TO BE UNKNOWN)
Duplication?EXAMPLE AEXAMPLE BDuplication?Duplication?Duplication5 METHODAmbiguous
69. TIGRTIGR
Arabidopsis thalianaGP9651815g
Drosophila melanogasterGP72929
Homo sapiensSPP49917DNL4 HUMAN
Gallus gallusGP15778121dbjBAB6
Xenopus laevisGP18029886gbAAL5
Candida albicansSPP52496DNLI C
Saccharomyces cerevisiaeGP1151
Schizosaccharomyces pombeGP700
Camelpox virusGP18483081gbAAL7
Variola major virusGP439074gbA
Cowpox virusGP20153167gbAAM136
Vaccinia virusGP2772802gbAAB96
VIRUS vaccinia 9791118refNP 06
Vaccinia virus strain Tian Tan
Monkeypox virusGP17529940gbAAL
Homo sapiensSPP49916DNL3 HUMAN
Mus musculusGP1794221gbAAC5300
Xenopus laevisGP18029884gbAAL5
lumpy skin disease virusGP1514
Swinepox virusGP18448623gbAAL6
Myxoma virusGP6523988gbAAF1502
Rabbit fibroma virusGP392838gb
Fowlpox virusGP453602embCAA828
Drosophila melanogasterGP72996
Arabidopsis thalianaSPQ42572DN
Oryza sativaGP16905197gbAAL310
Crithidia fasciculataGP312384e
Caenorhabditis elegansSPQ27474
Drosophila melanogasterGP72916
Homo sapiensSPP18858DNL1 HUMAN
Mus musculusSPP37913DNL1 MOUSE
Rattus norvecusSPQ9JHY8DNL1 RA
Xenopus laevisSPP51892DNL1 XEN
Plasmodium falciparumGP1815859
Schizosaccharomyces pombeSPP12
Saccharomyces cerevisiaeSPP048
Aeropyrum pernixSPQ9YD18DNLI A
Acidianus ambivalensSPQ02093DN
Sulfolobus solfataricusSPQ980T
Sulfolobus shibataeSPQ9P9K9DNL
Sulfolobus tokodaiiSPQ976G4DNL
Aquifex aeolicusGP2983805gbAAC
Aquifex aeolicusSPO67398DNLI A
Pyrobaculum aerophilumGP409906
uncultured crenarchaeote 74A4G
Thermoplasma acidophilumSPQ9HJ
Thermoplasma volcaniumOMNINTL0
Methanosarcina acetivorans str
Archaeoglobus fuldusSPO29632DN
A METAC 19916535gbAAM05952.1 D
Pyrococcus abyssiSPQ9V185DNLI
Pyrococcus horikoshiiSPO59288D
Pyrococcus furiosusSPP56709DNL
Thermococcus kodakaraensisGP10
Thermococcus fumicolansSPQ9HH0
Methanopyrus kandleri AV19GP19
Methanococcus jannaschiiSPQ576
Halobacterium sp.SPQ9HR35DNLI
Streptomyces coelicolorSPQ9FCB
Lymantria dispar nucleopolyhed
Ligase IV
Viral ligases
Ligase I
Archaeal Ligase
DNA Ligase Tree
70. TIGRTIGR
Problems with Similarity Based
Functional Prediction
• Prone to database error propagation.
• Cannot identify orthologous groups reliably.
• Perform poorly in cases of evolutionary rate variation and
non-hierarchical trees (similarity will not reflect evolutionary
relationships in these cases)
• May be misled by modular proteins or large
insertion/deletion events.
• Are not set up to deal with expanding data sets.
TIGRTIGR
73. TIGRTIGR
AlkA Domain (O6-Me-G glycosylase)Ogt Domain (O6-Me-G alkyltransferase)Ada Domain (transcriptions regulator)Ada E. coliAda H. inflOgt E. coliOgt H. inflOgt Gram+Ogt D. radioAlkA Gram+AlkA E. coliMGMT Euks
Alkylation Repair Genes
75. TIGRTIGR
Types of Molecular Homology
• Homologs: genes that are descended from a common ancestor (e.g.,
all globins)
• Orthologs: homologs that have diverged after speciation events (e.g.,
human and chimp β-globins)
• Paralogs: homologs that have diverged after gene duplication events
(e.g., α and β globin).
• Xenologs: homologs that have diverged after lateral transfer events
• Positional homology: common ancestry of specific amino acid or
nucleotide positions in different genes
76. TIGRTIGR
Caution: Homology Based
Predictions Have Many Flaws
• Not all orthologs have the same function
• Homology cannot be used to characterize
novel pathways (e.g., D. radiodurans)
• Absence of genes can be important to
phenotypes (e.g., pathogenicity)
80. TIGRTIGR
Unusual Features of D. radiodurans
DNA Repair Genes
Process Genes
Nucleotide excision repair Two UvrAs
Base excision repair Four MutY-Nths
Recombination RecD but not RecBC
Replication Four Pol genes
dNTP pools Many MutTs, two RRases
Other UVDE
81. TIGRTIGR
Problem:
List of DNA repair gene homologs
in D. radiodurans genome is not
significantly different from other
bacterial genomes of the similar size
82. TIGRTIGR
Repair Studies in Different Species
(determined by Medline searches as of 1998)
Humans 7028
E. coli 3926
S. cerevisiae 988
Drosophila 387
B. subtilits 284
S. pombe 116
Xenopus 56
C. elegans 25
A. thaliana 20
Methanogens 16
Haloferax 5
Giardia 0
88. TIGRTIGR
Chlorobium tepidum Strain TLS
C. tepidum mat in highly sulfidic
“Travelodge Stream”,
Rotorua, New Zealand
(from Castenholz and Pierson, 1995)
Phase contrast photomicrograph
of the 48-hours culture and electron
micrograph of thin cell section
(from Wahlund et al, 1991)
89. TIGRTIGR
Phylogenetic Profile -
C. tepidum Chlorophyll
Synthesis
Wu and Eisen, unpublished
5002_cobalamin biosynthesis protein CbiG/precorrin-4 C11-methyltransferase3939_precorrin-3B C17-methyltransferase/precorrin-8X methylmutase cbiJH882_cobyric acid synthase cbiP3160_dsrN protein dsrN862_cobyrinic acid a,c-diamide synthase cbiA-14010_cobN protein, putative2641_magnesium-protoporphyrin methyltransferase bchH-31498_magnesium-protoporphyrin methyltransferase bchH-14003_cobN protein, putative2636_magnesium-protoporphyrin methyltransferase bchH-24008_magnesium-chelatase, subunit I chlI-24007_magnesium-chelatase, subunit D/I family1504_magnesium-chelatase, subunit I chlI-1
93. TIGRTIGR
Uses of Phylogenomics
• Species evolution and systematics
• Lateral versus vertical evolution
• Gene function
• Gene and genome duplications
• Genome rearrangements
94. TIGRTIGR
Uses of Phylogenomics
• Species evolution and systematics
• Lateral versus vertical evolution
• Gene function
• Gene and genome duplications
• Genome rearrangements
95. TIGRTIGR
Why Duplications Are Useful to Identify
• Allows division into orthologs and paralogs
• Improves functional predictions
• Helps identify mechanisms of duplication
• Can be used to study mutation processes in
different parts of a genome
• Lineage specific duplications may be indicative
of species’ specific adaptations
96. TIGRTIGR
Levels of Paralogy Within A Genome
• All
– All members of a gene family are linked together
• Top matches
– Only top matching pairs are linked together.
Therefore, if in a large gene family, only the pair
from the most recent duplication event is included
• Recent
– Operational definition based on comparison to other
species. Only pairs which are more similar to each
other than to selected other species are included.
97. TIGRTIGR
C. pneumoniae Paralogs by Position
0
250000
500000
750000
1000000
1250000
Subject Orf Position
0 250000 500000 750000 1000000 1250000
Query Orf Position
98. TIGRTIGR
C. pneumoniae Paralogs -
Lineage Specific
0
250000
500000
750000
1000000
1250000
Subject Orf Position
0 250000 500000 750000 1000000 1250000
Query Orf Position
100. TIGRTIGR
B. anthracis lineage specific duplications
ORF04205 molybdopterin biosynthesis protein MoeA (moeA)
ORF05907 molybdopterin biosynthesis protein MoeA (moeA)
ORF02636 molybdopterin biosynthesis protein MoeA (moeA)
ORF04204 molybdopterin biosynthesis protein MoeB, putative
ORF05908 molybdopterin biosynthesis protein MoeB, putative
ORF02634 molybdopterin biosynthesis protein MoeB, putative
ORF05904 molybdopterin converting factor, subunit 1 (moaD)
ORF02639 molybdopterin converting factor, subunit 1 (moaD)
ORF04206 molybdopterin converting factor, subunit 2 (moaE)
ORF05905 molybdopterin converting factor, subunit 2 (moaE)
ORF02638 molybdopterin converting factor, subunit 2 (moaE)
Based on Read et al. submitted
101. TIGRTIGR
S. aureus Lineage Specific Duplications
ORF02715 4-diphosphocytidyl-2C-methyl-D-erythritol synthase, putative
ORF02712 alcohol dehydrogenase, zinc-containing
ORF00701 alpha-hemolysin precursor (2X)
ORF00717 antibacterial protein
ORF02597 capsular polysaccharide biosynthesis proteins CapABC (2X)
ORF00804 cell wall hydrolase (3X)
ORF00657 cell wall surface anchor family protein (2X)
ORF00358 clumping factor (2X)
ORF01758 deoxyribose-phosphate aldolase (deoC)
ORF02579 purine nucleoside phosphorylase (deoD)
ORF01031 drug transporter, putative
ORF00805 endopeptidase resistance gene (eprH)
ORF00706 exotoxin 1,3,4,5, unknown (2X)
ORF02184 fibronectin(2X)
ORF00097 glycosyl transferase, group 1 family protein (3X)
ORF02086 IgG-binding protein (2X)
ORF02431 integrase/recombinase, core domain family (3X)
Analysis done with S. Gill
102. TIGRTIGR
S. aureus Lineage Specific Duplications
ORF00137 conserved hypothetical protein
ORF00138 conserved hypothetical protein
ORF00139 conserved hypothetical protein
ORF00140 conserved hypothetical protein
ORF00141 conserved hypothetical protein
ORF00142 conserved hypothetical protein
ORF00143 conserved hypothetical protein
ORF00144 conserved hypothetical protein
ORF00145 conserved hypothetical protein
ORF00146 conserved hypothetical protein
ORF00148 conserved hypothetical protein
ORF00667 conserved hypothetical protein
ORF01251 conserved hypothetical protein
ORF02160 conserved hypothetical protein
ORF02166 conserved hypothetical protein
ORF02170 conserved hypothetical protein
ORF02171 conserved hypothetical protein
ORF02507 conserved hypothetical protein
ORF02745 conserved hypothetical protein
ORF02760 conserved hypothetical protein
ORF02762 conserved hypothetical protein
ORF02763 conserved hypothetical protein
ORF02766 conserved hypothetical protein
ORF02768 conserved hypothetical protein
ORF02769 conserved hypothetical protein
ORF02770 conserved hypothetical protein
ORF02771 conserved hypothetical protein
ORF02772 conserved hypothetical protein
ORF02773 conserved hypothetical protein
ORF02774 conserved hypothetical protein
ORF02896 conserved hypothetical protein
ORF02974 conserved hypothetical protein
ORF02711 conserved hypothetical protein UPF0007
ORF02614 conserved hypothetical protein, authentic frameshift
ORF00286 hypothetical protein
ORF00338 hypothetical protein
ORF00361 hypothetical protein
ORF00412 hypothetical protein
ORF00415 hypothetical protein
ORF00614 hypothetical protein
ORF00697 hypothetical protein
ORF00703 hypothetical protein
ORF00705 hypothetical protein
ORF00875 hypothetical protein
ORF00876 hypothetical protein
ORF00877 hypothetical protein
ORF00879 hypothetical protein
ORF00888 hypothetical protein
ORF00889 hypothetical protein
ORF01024 hypothetical protein
ORF01041 hypothetical protein
ORF01089 hypothetical protein
ORF01091 hypothetical protein
ORF01092 hypothetical protein
ORF01093 hypothetical protein
ORF01095 hypothetical protein
ORF01446 hypothetical protein
ORF01462 hypothetical protein
ORF01918 hypothetical protein
ORF02099 hypothetical protein
ORF02102 hypothetical protein
ORF02158 hypothetical protein
ORF02159 hypothetical protein
ORF02172 hypothetical protein
ORF02430 hypothetical protein
ORF02434 hypothetical protein
ORF02530 hypothetical protein
ORF02531 hypothetical protein
ORF02532 hypothetical protein
ORF02533 hypothetical protein
ORF02534 hypothetical protein
Analysis done with S. Gill
103. TIGRTIGR
Lineage Specific Duplications in Wolbachia wMel
Annotation
ankyrin repeat domain protein
ankyrin repeat domain protein
ankyrin repeat domain protein
ankyrin repeat domain protein
ankyrin repeat domain protein
ankyrin repeat domain protein
ankyrin repeat domain protein
conserved domain protein
conserved domain protein
conserved domain protein
conserved domain protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
conserved hypothetical protein
FRAMESHIFT
conserved hypothetical protein
POINT MUTATION
conserved hypothetical protein,
degenerate
conserved hypothetical protein,
FRAMESHIFT
conserved hypothetical protein,
FRAMESHIFT
conserved hypothetical protein,
FRAMESHIFT
conserved hypothetical protein,
FRAMESHIFT
conserved hypothetical protein,
interruption-C
conserved hypothetical protein,
POINT MUTATION
conserved hypothetical protein,
POINT MUTATION
conserved hypothetical protein,
truncated
conserved hypothetical protein,
truncation
DNA mismatch repair protein
MutL (mutL)
DNA repair protein RadC,
putative
DNA repair protein RadC,
putative, truncation
DNA repair protein RadC,
truncation
DnaJ domain protein
DnaJ domain protein
exopolysaccharide synthesis
protein ExoD-related protein
exopolysaccharide synthesis
protein ExoD-related protein
HNH endonuclease family
protein
HNH endonuclease family
protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
hypothetical protein
major facilitator family
transporter
major facilitator family
transporter
major facilitator family
transporter
membrane protein, putative
membrane protein, putative
membrane protein, putative
MutL family protein
Na+/H+ antiporter family protein
Na+/H+ antiporter, putative
permease, putative
portal protein, FRAMESHIFT
portal protein, FRAMESHIFT
prophage LambdaW1, DNA
methylase
prophage LambdaW1, terminase
large subunit, putative
prophage LambdaW2, ankyrin
repeat domain protein
prophage LambdaW2, ankyrin
repeat domain protein
prophage LambdaW2, baseplate
assembly protein J, putative
prophage LambdaW2, baseplate
assembly protein V, putative
FRAMESHIFT
prophage LambdaW2, baseplate
assembly protein V, putative
FRAMESHIFT
prophage LambdaW2, baseplate
assembly protein W, putative
prophage LambdaW2, minor tail
protein Z, putative,
FRAMESHIFT
prophage LambdaW2, site-
specific recombinase, resolvase
family
prophage LambdaW4, ankyrin
repeat domain protein
prophage LambdaW4, DNA
methylase
prophage LambdaW4, portal
protein, FRAMESHIFT
prophage LambdaW4, portal
protein, FRAMESHIFT
prophage LambdaW4, terminase
large subunit, putative
prophage LambdaW5, ankyrin
repeat domain protein
prophage LambdaW5, ankyrin
repeat domain protein
prophage LambdaW5, ankyrin
repeat domain protein
prophage LambdaW5, baseplate
assembly protein J, putative,
FRAMESHIFT
prophage LambdaW5, baseplate
assembly protein V, putative
prophage LambdaW5, baseplate
assembly protein W, putative
prophage LambdaW5, minor tail
protein Z, putative, degenerate,
FRAMESHIFT
prophage LambdaW5, site-
specific recombinase, resolvase
family
regulatory protein RepA, putative
regulatory protein RepA, putative
reverse transcriptase, putative
reverse transcriptase, putative
reverse transcriptase, putative
sodium/alanine symporter family
protein
sodium/alanine symporter family
protein
TenA/THI-4 family protein
transcriptional regulator
transcriptional regulator
transcriptional regulator
transcriptional regulator
transcriptional regulator
transcriptional regulator
transcriptional regulator, putative
translation elongation factor Tu
(tuf)
translation elongation factor Tu
(tuf)
transposase, degenerate
transposase, IS4 family
transposase, IS4 family
transposase, IS4 family
transposase, IS5 family,
interruption-N
transposase, IS5 family,
truncation
transposase, putative, degenerate
transposase, putative, degenerate
transposase, putative, degenerate
type IV secretion system protein
VirB4, putative
UDP-N-acetylglucosamine
pyrophosphorylase-related
protein
104. TIGRTIGR
MutL Duplication in Wolbachia wMel
ORF01096 DNA mismatch repair protein MutL (mutL)
ORF00446 MutL family protein
106. TIGRTIGR
Superoxide Dismutase Duplication
in D. radiodurans
D. radiodurans 2
D. radiodurans 1
V. cholerae
E. coli
M. tuburculosis
B. subtilis
A. aeolicus 1
A. aeolicus 2
C. elegans
Yeast
see White et al. (1999)
109. TIGRTIGR
Uses of Phylogenomics
• Species evolution and systematics
• Lateral versus vertical evolution
• Gene function
• Gene and genome duplications
• Genome rearrangements
110. TIGRTIGR
X-files
Eisen et al. 2000. Genome Biology 1(6): 11.1-11.9
Also see Tillier and Collins. 2000. Nature Genetics
26(2):195-7 and Suyama and Bork. 2001. Trends Genetics
17: 10-13.
111. TIGRTIGR
V. cholerae vs. E. coli All
0
1000000
2000000
3000000
4000000
5000000
E. coli
Coordinates
0 1000000 2000000 3000000
V. cholerae Coordinates
112. TIGRTIGR
V. cholerae vs. E. coli Best
0
1000000
2000000
3000000
4000000
5000000
E. coli
Coordinates
0 1000000 2000000 3000000
V. cholerae Coordinates
113. TIGRTIGR
V. cholerae vs. E. coli if Top
0
1000000
2000000
3000000
4000000
5000000
E. coli
Coordinates
0 1000000 2000000 3000000
V. cholerae Coordinates
114. TIGRTIGR
V. cholerae vs. E. coli
Top Matches, Rotated
0
1000000
2000000
3000000
4000000
5000000
E. coli
ORF Coordinates
0 500000 1000000 1500000 2000000 2500000 3000000
V. cholerae ORF Coordinates
115. TIGRTIGR
Duplication and Gene Loss Model
A
B
CD
E
F
A
B
CD
E
F
A
B
C
D
E
F
A
B
C
D
E
F
A’
B’
C’
D’
E’
F’
A
B
C
D
E
F
A’
B’
C’
D’
E’
F’
A
C
D
F
A’
B’
E’
E. coli
E. coli
B
C
D
F
A’
B’
D’
E’
V. cholerae
A
B
C
D
E
F
A’
B’
C’
D’
E’
F’
117. TIGRTIGR
V. cholerae vs. E. coli
Best Matching Proteins by Location
0
1000000
2000000
3000000
4000000
5000000
E. coli
ORF Coordinates
0 500000 1000000 1500000 2000000 2500000 3000000
V. cholerae ORF Coordinates
118. TIGRTIGR C. trachomatis MoPn
C.pneumoniaeAR39
Origin
Terminus
C. trachomatis vs C. pneumoniae Dot Plot
119. TIGRTIGR
M. leprae vs. M. tuberculosis Whole
Genome Alignment
0
1000000
2000000
3000000
4000000
Mycobacterium tuberculosis
0 1000000 2000000 3000000
Mycobacterium leprae
120. TIGRTIGR
B. subtilis vs. S. auerus
0
500
1000
1500
2000
2500
3000
2632200 2632700 2633200 2633700 2634200 2634700 2635200 2635700 2636200 2636700
analysis w/ S. Gill
121. TIGRTIGR
P. putida vs. P.aeruginosa Orthologs
9945700
9946700
9947700
9948700
9949700
9950700
9951700
0 2000 4000 6000 8000
Series1
analysis w/ K. Nelson
124. TIGRTIGR
Why are Inversions Symmetrical
Around Origin
• Genetic studies in Salmonella and E. coli
suggest that there may be strong selection
against other inversions
• See:
– Mahan, Segall, Schmid and Roth
– Liu and Sanderson
– Rebollo, Francois, and, Louarn