Microbial Phylogenomics (EVE161) at UC Davis Spring 2016. Co-taught by Jonathan Eisen and Holly Ganz.
Class 6:
Ear II: Culture independent rRNA studies
UC Davis EVE 161 Lecture 7 - rRNA workflows - by Jonathan Eisen @phylogenomicsJonathan Eisen
This document summarizes a lecture on rRNA sequencing and analysis from a microbiome phylogenomics course. The lecture covers:
- The goals that should guide rRNA analysis, including taxonomic assignment, ecological characterization of communities, and comparisons between communities.
- The general workflow for rRNA analysis, including PCR, sequencing, alignment, clustering sequences into OTUs, and assigning taxonomy to OTUs.
- Methods for measuring alpha and beta diversity from rRNA data, including OTU richness, phylogenetic diversity, and comparisons between communities.
- Specific techniques covered in more depth include degenerate PCR, alignment, OTU clustering, and diversity metrics like rarefaction curves and rank abundance curves.
UC Davis EVE161 Lecture 13 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on microbial phylogenomics from a winter 2014 course at UC Davis taught by Jonathan Eisen. The lecture covered several topics:
- Analysis of fungal genomes revealed over 200 genes specific to eukaryotes involved in cytoskeleton, protein degradation and chromatin. Few genes differentiated single-celled from multicellular eukaryotes.
- Endosymbiont genomes were found to evolve more rapidly than free-living relatives due to population genetics factors rather than DNA repair differences.
- Lateral gene transfer plays a major role in prokaryote evolution, occurring through transformation, conjugation and transduction. Whole genome trees and atypical gene distributions can reveal transfer
This document outlines the syllabus for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The course will cover the history of sequencing-based studies of microbial diversity through four eras: the rRNA tree of life, rRNA analysis of environmental samples, genome sequencing, and metagenomics. Students will learn about microbial diversity, phylogeny, and how to analyze research papers. The course will include lectures, readings, assignments, and a final student project to critically review a relevant research paper. Grading will be based on participation, weekly assignments, exams, a presentation, and a final exam.
UC Davis EVE161 Lecture 11 by @phylogenomicsJonathan Eisen
This document summarizes key points from Lecture 10 of the course Microbial Phylogenomics at UC Davis taught by Jonathan Eisen in Winter 2014. It discusses genome sequencing and comparative genomics. Specifically, it covers structural diversity of bacterial genomes including multiple genetic elements like plasmids and chromosomes. It also discusses gene content, order, density and shared genes between bacterial strains and species. Genome rearrangements through inversions or mobile elements inserting genomic islands are noted to contribute to genomic diversity.
This document summarizes key concepts from a lecture on the early development of the tree of life. It discusses how prior to Carl Woese's work in the 1960s-1970s, constructing a universal tree of life was difficult due to a lack of homologous traits shared across all domains of life. Woese developed one of the first universal trees using sequences of 16S ribosomal RNA, which are highly conserved yet vary enough between major groups to distinguish relationships. His work established the three domain system of Archaea, Bacteria, and Eukarya and provided strong evidence that all life on Earth descended from a common ancestor.
The document summarizes a lecture on the modern view of the tree of life. It discusses two papers for the lecture - one that analyzes the eukaryotic tree of life using broad taxonomic sampling, and one that places eukaryotes within the Archaea based on phylogenomic analysis. The lecture covers the parts of a phylogenetic tree, character analysis, data matrices, sequence alignment, tree reconstruction methods, and challenges like long branch attraction and homoplasy. It shows tree topologies from analyses using varying numbers of taxa.
This document contains slides from a lecture on the evolution of DNA sequencing technologies taught by Jonathan Eisen at UC Davis in winter 2014. The lecture covers the timeline of sequencing technology development from early manual Sanger and Maxam-Gilbert sequencing methods through modern next-generation sequencing platforms. It discusses the key innovations that enabled automation and high-throughput sequencing, such as labeled dideoxynucleotides, capillary electrophoresis, emulsion PCR, and sequencing by synthesis using reversible terminators. The slides illustrate sequencing workflows and compare different sequencing platforms such as 454, Illumina, SOLiD, and Helicos.
UC Davis EVE161 Lecture 10 by @phylogenomicsJonathan Eisen
The document summarizes key concepts from Lecture 10 of the Microbial Phylogenomics course taught by Jonathan Eisen in winter 2014. It discusses the history of genome sequencing, including the first bacterial genome sequenced. It then covers the general steps involved in genome sequencing projects, including library construction, random sequencing, closure, and annotation. Subsequent slides discuss trends in completed genomes over time, structural annotation of genes and features, functional annotation including Gene Ontology and enzyme classification, and methods for functional prediction such as membrane protein prediction and phylogeny-based approaches.
UC Davis EVE 161 Lecture 7 - rRNA workflows - by Jonathan Eisen @phylogenomicsJonathan Eisen
This document summarizes a lecture on rRNA sequencing and analysis from a microbiome phylogenomics course. The lecture covers:
- The goals that should guide rRNA analysis, including taxonomic assignment, ecological characterization of communities, and comparisons between communities.
- The general workflow for rRNA analysis, including PCR, sequencing, alignment, clustering sequences into OTUs, and assigning taxonomy to OTUs.
- Methods for measuring alpha and beta diversity from rRNA data, including OTU richness, phylogenetic diversity, and comparisons between communities.
- Specific techniques covered in more depth include degenerate PCR, alignment, OTU clustering, and diversity metrics like rarefaction curves and rank abundance curves.
UC Davis EVE161 Lecture 13 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on microbial phylogenomics from a winter 2014 course at UC Davis taught by Jonathan Eisen. The lecture covered several topics:
- Analysis of fungal genomes revealed over 200 genes specific to eukaryotes involved in cytoskeleton, protein degradation and chromatin. Few genes differentiated single-celled from multicellular eukaryotes.
- Endosymbiont genomes were found to evolve more rapidly than free-living relatives due to population genetics factors rather than DNA repair differences.
- Lateral gene transfer plays a major role in prokaryote evolution, occurring through transformation, conjugation and transduction. Whole genome trees and atypical gene distributions can reveal transfer
This document outlines the syllabus for a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2014. The course will cover the history of sequencing-based studies of microbial diversity through four eras: the rRNA tree of life, rRNA analysis of environmental samples, genome sequencing, and metagenomics. Students will learn about microbial diversity, phylogeny, and how to analyze research papers. The course will include lectures, readings, assignments, and a final student project to critically review a relevant research paper. Grading will be based on participation, weekly assignments, exams, a presentation, and a final exam.
UC Davis EVE161 Lecture 11 by @phylogenomicsJonathan Eisen
This document summarizes key points from Lecture 10 of the course Microbial Phylogenomics at UC Davis taught by Jonathan Eisen in Winter 2014. It discusses genome sequencing and comparative genomics. Specifically, it covers structural diversity of bacterial genomes including multiple genetic elements like plasmids and chromosomes. It also discusses gene content, order, density and shared genes between bacterial strains and species. Genome rearrangements through inversions or mobile elements inserting genomic islands are noted to contribute to genomic diversity.
This document summarizes key concepts from a lecture on the early development of the tree of life. It discusses how prior to Carl Woese's work in the 1960s-1970s, constructing a universal tree of life was difficult due to a lack of homologous traits shared across all domains of life. Woese developed one of the first universal trees using sequences of 16S ribosomal RNA, which are highly conserved yet vary enough between major groups to distinguish relationships. His work established the three domain system of Archaea, Bacteria, and Eukarya and provided strong evidence that all life on Earth descended from a common ancestor.
The document summarizes a lecture on the modern view of the tree of life. It discusses two papers for the lecture - one that analyzes the eukaryotic tree of life using broad taxonomic sampling, and one that places eukaryotes within the Archaea based on phylogenomic analysis. The lecture covers the parts of a phylogenetic tree, character analysis, data matrices, sequence alignment, tree reconstruction methods, and challenges like long branch attraction and homoplasy. It shows tree topologies from analyses using varying numbers of taxa.
This document contains slides from a lecture on the evolution of DNA sequencing technologies taught by Jonathan Eisen at UC Davis in winter 2014. The lecture covers the timeline of sequencing technology development from early manual Sanger and Maxam-Gilbert sequencing methods through modern next-generation sequencing platforms. It discusses the key innovations that enabled automation and high-throughput sequencing, such as labeled dideoxynucleotides, capillary electrophoresis, emulsion PCR, and sequencing by synthesis using reversible terminators. The slides illustrate sequencing workflows and compare different sequencing platforms such as 454, Illumina, SOLiD, and Helicos.
UC Davis EVE161 Lecture 10 by @phylogenomicsJonathan Eisen
The document summarizes key concepts from Lecture 10 of the Microbial Phylogenomics course taught by Jonathan Eisen in winter 2014. It discusses the history of genome sequencing, including the first bacterial genome sequenced. It then covers the general steps involved in genome sequencing projects, including library construction, random sequencing, closure, and annotation. Subsequent slides discuss trends in completed genomes over time, structural annotation of genes and features, functional annotation including Gene Ontology and enzyme classification, and methods for functional prediction such as membrane protein prediction and phylogeny-based approaches.
UC Davis EVE161 Lecture 8 - rRNA ecology - by Jonathan Eisen @phylogenomicsJonathan Eisen
This lecture discusses using rRNA sequencing to analyze and compare microbial communities between different environmental samples. It introduces UniFrac, a new phylogenetic method for measuring distances between communities based on shared lineages. UniFrac can be used to compare multiple samples simultaneously and is more powerful than previous non-phylogenetic techniques because it accounts for evolutionary distances between sequences. The lecture applies UniFrac to compare bacterial populations in different marine environments like water, sediment, and sea ice to examine questions about culturing effects, bacterial cosmopolitanism, and habitat distinctions.
This document appears to be a set of lecture slides for a microbiology phylogenomics course taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss lecture 5 on culture-independent rRNA analysis from environmental samples and preview the next lecture on PCR and major phylogenetic groups. Students are assigned a short quiz and take-home assignment on a specific paper discussing archaeal origins of eukaryotes. Three papers are also outlined for discussion in the lecture.
UC Davis EVE161 Lecture 17 by @phylogenomicsJonathan Eisen
This document contains slides from a lecture on metagenomics given by Jonathan Eisen at UC Davis in winter 2014. The lecture discusses shotgun metagenomics and analyzing metagenomic functions and gene content from environmental samples without genome assemblies. It provides an example of a comparative metagenomics study of various microbial communities that identified habitat-specific genes and metabolic profiles reflecting the different environments. The slides include figures and references from a 2005 Science paper on this topic. Problem set 4 for the class involves selecting a relevant paper for presentation the following week.
UC Davis EVE161 Lecture 16 by @phylogenomicsJonathan Eisen
The document appears to be slides from a lecture on microbial phylogenomics given by Jonathan Eisen at UC Davis in winter 2014. It discusses using metagenomic shotgun sequencing and phylogenetic analysis of marker genes to study microbial diversity and classify unknown microbes from environmental samples without reference genomes. Specifically, it describes using this approach to study the bacterial symbionts of the glassy-winged sharpshooter, which transmits a plant pathogen.
The document discusses a lecture on microbial diversity. It notes that the tree of life is mostly microbial, diverse methods exist to study microbial diversity, and most microbial diversity remains poorly characterized. Sequencing methods like rRNA and metagenomic sequencing have improved understanding of microbial phylogeny but much diversity remains unknown.
The document is a set of slides for a lecture on the Tree of Life. It discusses evidence that all life on Earth is related, including universal traits like the genetic code and cell structure. It covers historical models of the Tree of Life from Darwin to the modern understanding based on Carl Woese's work comparing rRNA sequences. Woese's RNA-based tree supported the division of life into Bacteria, Archaea, and Eukarya domains, reflecting a more complex early evolution than previously thought.
BIS2C: Lecture 35: Symbioses Across the Tree of LifeJonathan Eisen
This document outlines a lecture on interactions across the tree of life. It discusses how the course is organized based on the tree of life and phylogeny. It provides examples of symbiotic relationships between organisms, such as the relationship between the Xylella fastidiosa bacterium, grapes, and the glassy-winged sharpshooter vector. It also describes the complex coevolution between plants and the insects that feed on them, and how insects have adapted to overcome plant defenses by developing symbiotic relationships with microbes.
The document contains slides from a lecture on fungi. It discusses the evolution of fungi and their diversity of forms. It covers fungal reproduction, life styles including parasitic, mutualistic and saprobic, and various uses of fungi in food, industry and pharmaceuticals. It provides examples of important mutualistic fungi like mycorrhizae and lichens. It also discusses the discovery of penicillin from the fungus Penicillium notatum.
This document contains slides from a lecture on chordates and vertebrate evolution. The slides cover topics like the phylogeny of chordates and vertebrates, innovations in vertebrate evolution like jaws and limbs, and examples of key vertebrate groups like lampreys and hagfish. The document emphasizes how scientists use comparative biology and phylogenetic trees to study relationships between organisms and infer ancestral traits.
The document contains slides from a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2016. The slides discuss various topics relating to metagenomics including the environmental genome shotgun sequencing of the Sargasso Sea, methods for binning sequences from metagenomic data like aligning to reference genomes or assembly, and examples of projects that used shotgun sequencing like the Wolbachia and glassy-winged sharpshooter projects. It also discusses challenges with assembly for metagenomic data due to variations in coverage and the DeLong lab's early work characterizing uncultured marine microbes.
This document contains slides from a lecture on triploblasts and lophotrochozoans. It discusses the key features of lophotrochozoans like their lophophore and trochophore larval stages. Major groups within the lophotrochozoans are discussed like mollusks and annelids. Examples of mollusks like cephalopods are described in more detail, highlighting characteristics like their advanced vision and ability to change appearance. Annelid examples discussed include pogonophorans that live at hydrothermal vents and rely on bacterial symbionts for nutrition.
This document contains slides from a lecture on chordates. It discusses the key characteristics of chordates like the notochord and dorsal hollow nerve cord. It covers the three major chordate groups: lancelets, tunicates, and vertebrates. Lancelets retain many chordate features throughout life. Tunicates resemble chordates as larvae but undergo metamorphosis and lose most features as adults. Many slides show examples of symbiosis in chordates and other animals.
BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 7.
Introduction to Microbial Diversity.
Slides for Lectures by Jonathan Eisen
UC Davis EVE161 Lecture 15 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on shotgun metagenomics from a course on microbial phylogenomics. The lecture discusses how shotgun sequencing was applied to sequence microbial communities directly from environmental samples, without culturing. This allowed reconstruction of near-complete genomes from dominant species in an acid mine drainage biofilm sample. The sample was dominated by a few microbial populations, and shotgun sequencing generated enough data to assemble genomes representing Leptospirillum group II and Ferroplasma type II. Analysis of the assembled genomes provided insights into the metabolic pathways and survival strategies of these uncultivated organisms inhabiting an extreme environment.
UC Davis EVE161 Lecture 8 - rRNA ecology - by Jonathan Eisen @phylogenomicsJonathan Eisen
This lecture discusses using rRNA sequencing to analyze and compare microbial communities between different environmental samples. It introduces UniFrac, a new phylogenetic method for measuring distances between communities based on shared lineages. UniFrac can be used to compare multiple samples simultaneously and is more powerful than previous non-phylogenetic techniques because it accounts for evolutionary distances between sequences. The lecture applies UniFrac to compare bacterial populations in different marine environments like water, sediment, and sea ice to examine questions about culturing effects, bacterial cosmopolitanism, and habitat distinctions.
This document appears to be a set of lecture slides for a microbiology phylogenomics course taught by Jonathan Eisen at UC Davis in winter 2014. The slides discuss lecture 5 on culture-independent rRNA analysis from environmental samples and preview the next lecture on PCR and major phylogenetic groups. Students are assigned a short quiz and take-home assignment on a specific paper discussing archaeal origins of eukaryotes. Three papers are also outlined for discussion in the lecture.
UC Davis EVE161 Lecture 17 by @phylogenomicsJonathan Eisen
This document contains slides from a lecture on metagenomics given by Jonathan Eisen at UC Davis in winter 2014. The lecture discusses shotgun metagenomics and analyzing metagenomic functions and gene content from environmental samples without genome assemblies. It provides an example of a comparative metagenomics study of various microbial communities that identified habitat-specific genes and metabolic profiles reflecting the different environments. The slides include figures and references from a 2005 Science paper on this topic. Problem set 4 for the class involves selecting a relevant paper for presentation the following week.
UC Davis EVE161 Lecture 16 by @phylogenomicsJonathan Eisen
The document appears to be slides from a lecture on microbial phylogenomics given by Jonathan Eisen at UC Davis in winter 2014. It discusses using metagenomic shotgun sequencing and phylogenetic analysis of marker genes to study microbial diversity and classify unknown microbes from environmental samples without reference genomes. Specifically, it describes using this approach to study the bacterial symbionts of the glassy-winged sharpshooter, which transmits a plant pathogen.
The document discusses a lecture on microbial diversity. It notes that the tree of life is mostly microbial, diverse methods exist to study microbial diversity, and most microbial diversity remains poorly characterized. Sequencing methods like rRNA and metagenomic sequencing have improved understanding of microbial phylogeny but much diversity remains unknown.
The document is a set of slides for a lecture on the Tree of Life. It discusses evidence that all life on Earth is related, including universal traits like the genetic code and cell structure. It covers historical models of the Tree of Life from Darwin to the modern understanding based on Carl Woese's work comparing rRNA sequences. Woese's RNA-based tree supported the division of life into Bacteria, Archaea, and Eukarya domains, reflecting a more complex early evolution than previously thought.
BIS2C: Lecture 35: Symbioses Across the Tree of LifeJonathan Eisen
This document outlines a lecture on interactions across the tree of life. It discusses how the course is organized based on the tree of life and phylogeny. It provides examples of symbiotic relationships between organisms, such as the relationship between the Xylella fastidiosa bacterium, grapes, and the glassy-winged sharpshooter vector. It also describes the complex coevolution between plants and the insects that feed on them, and how insects have adapted to overcome plant defenses by developing symbiotic relationships with microbes.
The document contains slides from a lecture on fungi. It discusses the evolution of fungi and their diversity of forms. It covers fungal reproduction, life styles including parasitic, mutualistic and saprobic, and various uses of fungi in food, industry and pharmaceuticals. It provides examples of important mutualistic fungi like mycorrhizae and lichens. It also discusses the discovery of penicillin from the fungus Penicillium notatum.
This document contains slides from a lecture on chordates and vertebrate evolution. The slides cover topics like the phylogeny of chordates and vertebrates, innovations in vertebrate evolution like jaws and limbs, and examples of key vertebrate groups like lampreys and hagfish. The document emphasizes how scientists use comparative biology and phylogenetic trees to study relationships between organisms and infer ancestral traits.
The document contains slides from a course on microbial phylogenomics taught by Jonathan Eisen at UC Davis in winter 2016. The slides discuss various topics relating to metagenomics including the environmental genome shotgun sequencing of the Sargasso Sea, methods for binning sequences from metagenomic data like aligning to reference genomes or assembly, and examples of projects that used shotgun sequencing like the Wolbachia and glassy-winged sharpshooter projects. It also discusses challenges with assembly for metagenomic data due to variations in coverage and the DeLong lab's early work characterizing uncultured marine microbes.
This document contains slides from a lecture on triploblasts and lophotrochozoans. It discusses the key features of lophotrochozoans like their lophophore and trochophore larval stages. Major groups within the lophotrochozoans are discussed like mollusks and annelids. Examples of mollusks like cephalopods are described in more detail, highlighting characteristics like their advanced vision and ability to change appearance. Annelid examples discussed include pogonophorans that live at hydrothermal vents and rely on bacterial symbionts for nutrition.
This document contains slides from a lecture on chordates. It discusses the key characteristics of chordates like the notochord and dorsal hollow nerve cord. It covers the three major chordate groups: lancelets, tunicates, and vertebrates. Lancelets retain many chordate features throughout life. Tunicates resemble chordates as larvae but undergo metamorphosis and lose most features as adults. Many slides show examples of symbiosis in chordates and other animals.
BIS2C. Biodiversity and the Tree of Life. 2014. L7. Intro to Microbial Divers...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 7.
Introduction to Microbial Diversity.
Slides for Lectures by Jonathan Eisen
UC Davis EVE161 Lecture 15 by @phylogenomicsJonathan Eisen
This document summarizes a lecture on shotgun metagenomics from a course on microbial phylogenomics. The lecture discusses how shotgun sequencing was applied to sequence microbial communities directly from environmental samples, without culturing. This allowed reconstruction of near-complete genomes from dominant species in an acid mine drainage biofilm sample. The sample was dominated by a few microbial populations, and shotgun sequencing generated enough data to assemble genomes representing Leptospirillum group II and Ferroplasma type II. Analysis of the assembled genomes provided insights into the metabolic pathways and survival strategies of these uncultivated organisms inhabiting an extreme environment.
The document summarizes a lecture on the human microbiome. It discusses how humans are colonized by vast numbers of microbes, forming complex microbial ecosystems. There is enormous variation in microbiome composition both within and between individuals, and this variation is associated with health states and phenotypes. Research has identified some possible causes of microbiome variation and suggests it may be possible to alter or restore microbiome composition.
Unit 1. How to measure diversity
LECTURE LEARNING GOALS
1. Describe the abundance and diversity of microbes, the “unseen majority”, in all natural and manufactured environments.
2. Explain the common measures of microbial diversity, and how diversity is measured.
3. What is the purpose of diversity?
Genetics chapter 7 dna structure and replicationvanessawhitehawk
The document summarizes key discoveries related to DNA as the genetic material. It describes early evidence that DNA is the molecule responsible for heredity, including Griffith's experiments showing transformation of bacteria with heat-killed DNA and Avery, MacLeod, and McCarty's experiments showing DNA is the transforming principle. It also summarizes Hershey and Chase's experiments demonstrating that DNA enters the host bacterial cell during viral infection. The document then covers Watson and Crick's discovery of the double helix structure of DNA and key features like base pairing and the sugar-phosphate backbone. It also summarizes semiconservative replication of DNA and key molecules involved like DNA polymerase, primers, and proofreading. Finally, it discusses telomer
Microbiome research is undergoing a crisis due to issues like the correlation-causation fallacy in studies and poor experimental design. The document discusses challenges with studying the microbiome, including biases and errors introduced from DNA extraction methods, sample storage conditions, and contamination from extraction kits. It emphasizes that every step in microbiome research, from sample collection to analysis, needs careful consideration to draw accurate conclusions.
The document provides information about DNA and the process of DNA replication:
- DNA is made up of nucleotides containing phosphate, deoxyribose sugar, and nitrogenous bases (adenine, guanine, cytosine, thymine). The bases bond together in pairs to form the double helix structure.
- DNA replication occurs during the S phase of the cell cycle to make an identical copy of DNA before the cell divides. It begins at origins of replication and proceeds bidirectionally.
- The two DNA strands separate and each acts as a template for new complementary strands. The leading strand is synthesized continuously while the lagging strand is synthesized in short fragments that are later joined.
This document discusses opportunities and challenges presented by next-generation DNA sequencing technologies. It begins by introducing the speaker, C. Titus Brown, and their commitment to open science. It then describes the dramatic decreases in cost and increases in scale of DNA sequencing. While this enables sequencing entire genomes and environmental samples, it presents challenges for analysis due to lack of reference genomes and limited computational tools. The document outlines goals for shotgun sequencing analysis and challenges for non-model organisms. It concludes by emphasizing the need for training in data analysis to take advantage of the vast amounts of sequencing data being generated.
The document discusses molecular evolution before the last universal common ancestor (LUCA). It outlines Peter Gogarten's presentation on gene duplications, properties of LUCA, the history of the translation machinery and genetic code expansion, the ribosomal tree of life and inferred optimal growth temperatures, tree shape artifacts, and phylogenetic evidence for LUCA's contemporaries. The presentation aims to provide insights into early evolution before the divergence of the bacterial and archaeal domains.
My talk to the PhD students NRP at the Doctoral Training Programme Summer Conference 2015, The Assembly House, Norwich, Thursday 18th June.
Notes and acknowledgments at http://kamounlab.tumblr.com/post/121748816600/what-are-world-class-science-outputs
DNA replication is semiconservative and bidirectional. It involves unwinding the parental DNA strands at an origin of replication followed by synthesis of new complementary strands. Each parental strand serves as a template for a new daughter strand. DNA polymerase adds nucleotides to the 3' end of the growing strand based on complementary base pairing. The leading strand is synthesized continuously while the lagging strand is synthesized discontinuously in short segments called Okazaki fragments. RNA primers are required for initiation and DNA polymerase proofreads and corrects errors to ensure high fidelity. Telomeres and the telomerase enzyme allow complete replication of linear chromosomes.
"The Quest for A field Guide to the Microbes" talk by Jonathan Eisen February...Jonathan Eisen
The document discusses the author's quest to create a field guide to microbes. It describes the challenges in doing so given microbes' small size and high diversity. The author discusses using DNA sequencing and phylogenetic trees to identify microbes and determine their functions and relationships. Examples are given of using DNA to study human microbiomes, forensic analysis, and microbial communities. The need for a comprehensive field guide is argued to better understand the roles and identification of microbes.
This document discusses key experiments that identified DNA as the genetic material, including Griffith's transformation experiment, Avery's experiment demonstrating that DNA was the transforming agent, and the Hershey-Chase experiment showing that DNA enters host cells during viral infection while proteins do not. It also describes the composition of nucleotides, the double helix structure of DNA proposed by Watson and Crick, and that DNA can take different conformations like A, B, and Z-DNA. RNA is also summarized as being similar in structure to DNA but containing uracil instead of thymine and generally being single-stranded.
This document discusses key experiments that identified DNA as the genetic material, including Griffith's transformation experiment, Avery's experiment demonstrating that DNA was the transforming agent, and the Hershey-Chase experiment showing that DNA enters host cells during viral infection while proteins do not. It also describes the composition of nucleotides, the double helix structure of DNA proposed by Watson and Crick, and that DNA can take different conformations like A, B, and Z-DNA. RNA is also summarized as being similar in structure to DNA but containing uracil instead of thymine and generally being single-stranded.
BIS2C. Biodiversity and the Tree of Life. 2014. L12. Symbioses and the Human ...Jonathan Eisen
This document contains lecture slides about symbiosis and the human microbiome. It discusses the evolution of the human microbiome and how history is important for understanding ecosystems. It also summarizes some of the key functions of the microbiome, including digestion, immune system management, and vitamin production. Finally, it outlines different types of symbiotic relationships and provides examples of pathogenic bacteria and eukaryotes.
April 14 2011 talk by Rosie Redfield at the University of Louisville. Title" What I learned from #arseniclife: communication and quality control in science
BIS2C_2020. Lecture 7. The Domains of Life.Jonathan Eisen
This document contains slides from a lecture on the domains of life. It discusses the three domain tree of life proposed by Carl Woese based on rRNA comparisons. Key results were that defining "prokaryotes" as a group renders it non-monophyletic, and that there are two major monophyletic groups of prokaryotes, termed Prokaryotic G1 and Prokaryotic G2. The slides focus on these results from Woese's rRNA tree regarding the relationships between organisms and the structure of the tree of life.
Similar to Microbial Phylogenomics (EVE161) Class 6: Era II - Culture Independent rRNA (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.
The cost of acquiring information by natural selectionCarl Bergstrom
This is a short talk that I gave at the Banff International Research Station workshop on Modeling and Theory in Population Biology. The idea is to try to understand how the burden of natural selection relates to the amount of information that selection puts into the genome.
It's based on the first part of this research paper:
The cost of information acquisition by natural selection
Ryan Seamus McGee, Olivia Kosterlitz, Artem Kaznatcheev, Benjamin Kerr, Carl T. Bergstrom
bioRxiv 2022.07.02.498577; doi: https://doi.org/10.1101/2022.07.02.498577
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.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...Sérgio Sacani
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...Leonel Morgado
Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
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.
ESA/ACT Science Coffee: Diego Blas - Gravitational wave detection with orbita...Advanced-Concepts-Team
Presentation in the Science Coffee of the Advanced Concepts Team of the European Space Agency on the 07.06.2024.
Speaker: Diego Blas (IFAE/ICREA)
Title: Gravitational wave detection with orbital motion of Moon and artificial
Abstract:
In this talk I will describe some recent ideas to find gravitational waves from supermassive black holes or of primordial origin by studying their secular effect on the orbital motion of the Moon or satellites that are laser ranged.
PPT on Direct Seeded Rice presented at the three-day 'Training and Validation Workshop on Modules of Climate Smart Agriculture (CSA) Technologies in South Asia' workshop on April 22, 2024.
The binding of cosmological structures by massless topological defectsSérgio Sacani
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
hematic appreciation test is a psychological assessment tool used to measure an individual's appreciation and understanding of specific themes or topics. This test helps to evaluate an individual's ability to connect different ideas and concepts within a given theme, as well as their overall comprehension and interpretation skills. The results of the test can provide valuable insights into an individual's cognitive abilities, creativity, and critical thinking skills
THEMATIC APPERCEPTION TEST(TAT) cognitive abilities, creativity, and critic...
Microbial Phylogenomics (EVE161) Class 6: Era II - Culture Independent rRNA
1. Lecture 6:
EVE 161:
Microbial Phylogenomics
Lecture 6:
Era II: Culture Independent rRNA
UC Davis, Winter 2016
Instructors: Jonathan Eisen & Holly Ganz
2. Where we are going and where we have been
• Previous lecture:
!5. Modern view of Tree of Life
• Current Lecture:
!6. Era II: rRNA from environment
• Next Lecture:
!7: Era II: rRNA PCR
!2
3. • Problem set on archaea vs. eukaryote phylogeny papers
will be posted today or emailed
!3