The document discusses DNA sequencing and its role in revolutionizing studies of microbial diversity. It describes how genome sequencing allowed researchers to characterize microbial genomes and better understand microbial metabolism, evolution, and diversity. It also discusses how sequencing enabled new approaches like metagenomics to characterize uncultured microbes directly from environmental samples using DNA analysis. Overall, the document outlines how genomic techniques like sequencing transformed microbiology by revealing new insights into microbial communities and functions.
This document describes how the Beast isolated his own DNA to understand his mutations and abilities. It provides instructions on how to extract DNA using common household materials like salt solution, detergent, and cold rubbing alcohol. The document suggests the Beast found mutations in his DNA that unlocked unique abilities. It prompts questions about experimenting with different DNA sources and how understanding his own mutations could help the Beast. The overall summary is that the document gives directions for a DNA extraction craft and discusses how the Beast analyzed his own DNA to discover the source of his powers and abnormalities.
Levin building ecology at Sloan Symposium, 2011hlevin
This document summarizes a presentation on linking microbial ecology with the indoor environment and building science. It identifies several key factors that can influence the microbial ecology within buildings:
1. Humidity, temperature, ventilation, and the surfaces of building materials are strongly connected to the microbes present indoors.
2. Filtration, cleaning practices, HVAC systems, envelope design, and maintenance are also important building components or processes that have plausible connections to indoor microbes.
3. Additional factors like building location, type, materials, room activities, and light exposure may also impact the indoor microbial ecology but require more research to establish clear connections. Understanding these interactions is important to characterize the complex indoor microbial environment
Microbiology is the study of microorganisms and their interactions with other organisms. This document discusses different types of symbiotic relationships between microorganisms such as mutualism, commensalism, neutralism, and parasitism. It also describes the indigenous microbiota that naturally inhabit different parts of the human body like the skin, gastrointestinal tract, and genitourinary system. These microorganisms play an important role in processes like nutrient cycling and soil fertility.
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 describes how the Beast isolated his own DNA to understand his mutations and abilities. It provides instructions on how to extract DNA using common household materials like salt solution, detergent, and cold rubbing alcohol. The document suggests the Beast found mutations in his DNA that unlocked unique abilities. It prompts questions about experimenting with different DNA sources and how understanding his own mutations could help the Beast. The overall summary is that the document gives directions for a DNA extraction craft and discusses how the Beast analyzed his own DNA to discover the source of his powers and abnormalities.
Levin building ecology at Sloan Symposium, 2011hlevin
This document summarizes a presentation on linking microbial ecology with the indoor environment and building science. It identifies several key factors that can influence the microbial ecology within buildings:
1. Humidity, temperature, ventilation, and the surfaces of building materials are strongly connected to the microbes present indoors.
2. Filtration, cleaning practices, HVAC systems, envelope design, and maintenance are also important building components or processes that have plausible connections to indoor microbes.
3. Additional factors like building location, type, materials, room activities, and light exposure may also impact the indoor microbial ecology but require more research to establish clear connections. Understanding these interactions is important to characterize the complex indoor microbial environment
Microbiology is the study of microorganisms and their interactions with other organisms. This document discusses different types of symbiotic relationships between microorganisms such as mutualism, commensalism, neutralism, and parasitism. It also describes the indigenous microbiota that naturally inhabit different parts of the human body like the skin, gastrointestinal tract, and genitourinary system. These microorganisms play an important role in processes like nutrient cycling and soil fertility.
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.
Evolution of microbiomes and the evolution of the study and politics of micro...Jonathan Eisen
The document discusses the evolution of microbiomes and the study of microbiomes. It notes that microbiomes can be both overhyped yet underappreciated. It provides background on the rise of interest in microbiomes since the 2000s due to technological advances enabling their study as well as appreciation of their important functions. The author then discusses their own research focusing on using phylogenomic methods to study microbial communities and symbioses, especially how microbes and microbiomes help hosts adapt to stress. Examples discussed include chemosymbioses, pathogen resistance, environmental changes, and more.
A renewed need for a genomic field guide to microbesJonathan Eisen
This document discusses the need for a genomic field guide to microbes. It outlines several challenges to creating such a guide, including the small size and diversity of microbes, as well as difficulties observing and collecting data on them in natural environments. Potential solutions proposed include advances in DNA sequencing technologies that have enabled large-scale cataloging and identification of microbes. Components suggested for inclusion in a field guide are phylogenetic catalogs, functional profiles, biogeography data, identification methods, and information on applications like pathogen detection. Citizen science initiatives are also presented as a way to engage the public in microbiology. The talk concludes by advocating the creation of a comprehensive genomic field guide to microbes.
The document contains slides from a lecture on fungi. The slides cover various topics about fungi, including their phylogenetic diversity, forms, and life cycles. Key points include that fungi have chitin in their cell walls, absorb nutrients from outside their bodies, and can have both single-celled and multicellular stages. The slides also discuss the different life cycles of groups like chytrids, which have flagellated spores and gametes to aid dispersal.
The document contains slides from a lecture on fungi. It discusses the life cycles of various fungi groups like zygospore fungi and basidiomycota. For zygospore fungi, plasmogamy (fusion of cells) precedes karyogamy (fusion of nuclei), allowing the fungi to exist in a dikaryotic state for a long period. For basidiomycota, the life cycle involves a haploid, dikaryotic, and diploid stage with fruiting bodies made of dikaryotic mycelia containing basidia that produce haploid basidiospores. The document also covers key innovations in fungi like the expanded dikaryon stage in dikarya
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.
Evolution of microbiomes and the evolution of the study and politics of micro...Jonathan Eisen
The document discusses the evolution of microbiomes and the study of microbiomes. It notes that microbiomes can be both overhyped yet underappreciated. It provides background on the rise of interest in microbiomes since the 2000s due to technological advances enabling their study as well as appreciation of their important functions. The author then discusses their own research focusing on using phylogenomic methods to study microbial communities and symbioses, especially how microbes and microbiomes help hosts adapt to stress. Examples discussed include chemosymbioses, pathogen resistance, environmental changes, and more.
A renewed need for a genomic field guide to microbesJonathan Eisen
This document discusses the need for a genomic field guide to microbes. It outlines several challenges to creating such a guide, including the small size and diversity of microbes, as well as difficulties observing and collecting data on them in natural environments. Potential solutions proposed include advances in DNA sequencing technologies that have enabled large-scale cataloging and identification of microbes. Components suggested for inclusion in a field guide are phylogenetic catalogs, functional profiles, biogeography data, identification methods, and information on applications like pathogen detection. Citizen science initiatives are also presented as a way to engage the public in microbiology. The talk concludes by advocating the creation of a comprehensive genomic field guide to microbes.
The document contains slides from a lecture on fungi. The slides cover various topics about fungi, including their phylogenetic diversity, forms, and life cycles. Key points include that fungi have chitin in their cell walls, absorb nutrients from outside their bodies, and can have both single-celled and multicellular stages. The slides also discuss the different life cycles of groups like chytrids, which have flagellated spores and gametes to aid dispersal.
The document contains slides from a lecture on fungi. It discusses the life cycles of various fungi groups like zygospore fungi and basidiomycota. For zygospore fungi, plasmogamy (fusion of cells) precedes karyogamy (fusion of nuclei), allowing the fungi to exist in a dikaryotic state for a long period. For basidiomycota, the life cycle involves a haploid, dikaryotic, and diploid stage with fruiting bodies made of dikaryotic mycelia containing basidia that produce haploid basidiospores. The document also covers key innovations in fungi like the expanded dikaryon stage in dikarya
DNA Sequencing and the Modern Revolution in Studies of Microbial Diversity
1. DNA Sequencing
and the
Modern Revolution in
Studies of Microbial Diversity
Jonathan A. Eisen
UC Davis
Talk at Calacademy
December 17, 2010
1
Monday, November 26, 12
5. Outline
• Introduction: Diversity of microbes
• I: The Tree of Life
• II: Genome Sequencing
• III: Microbes in the Field
• IV: Metagenomics
5
Monday, November 26, 12
6. Introduction
Diversity of Microbes
6
Monday, November 26, 12
7. D. Diversity of form
Diversity of function
7
Monday, November 26, 12
17. Diversity of form II: complexity and size
17
Monday, November 26, 12
18. Fruiting bodies
Photo 26.24 Fruiting body of gliding bacterium Stigmatella aurantiaca. SEM. 18
Monday, November 26, 12
19. Diversity of form III: biofilms
Attraction of
Free-swimming Signal other organisms
prokaryotes molecules
Binding to surface Matrix
Signal
molecules
Single-species biofilm
Irreversible attachment
Growth and division,
formation of matrix
Mature biofilm
19
Monday, November 26, 12
20. D. Diversity of form
Diversity of form:
microbial eukaryotes
20
Monday, November 26, 12
21. Part I:
The Tree of Life
21
Monday, November 26, 12
22. Darwin and a Single Tree of Life
George Richmond. Darwin Heirlooms Trust
Darwin Origin of Species 1859
Set stage for “tree thinking”
22
Monday, November 26, 12
23. Ernst Haeckel 1866
Plantae
Protista
Animalia
23
www.mblwhoilibrary.org
Monday, November 26, 12
24. Whittaker – Five Kingdoms 1969
Monera
Protista
Plantae
Fungi
Animalia
24
Monday, November 26, 12
25. The Microbe Problem
Most trees of life did not deal with microbes very
well
Trees were not based on comparing homologous
traits between all organisms
Monday, November 26, 12
29. rRNA Systematics
• All cellular organisms have ribosomes
• All have homologous subunits of the ribosomes including specific
ribosomal proteins and ribosomal RNAs (i.e., these are universally
homologous genes)
• Woese determined the sequences of ribosomal RNAs from different
species
• The sequences are highly similar but have some variation
• Each position in a rRNA can be considered a distinct character trait
• Each position has multiple possible character states (A, C, U, G)
29
Monday, November 26, 12
30. Alignments
• Method of assigning
homology to
individual residues
in different
sequences
• Allows one to have
multiple traits within
individual genes
• Each column in
alignment = a
different character
• Each residue
(ACTG) = state
30
Monday, November 26, 12
31. Alignments
• Similar in
concept to lining
up bones from
different
species
31
Monday, November 26, 12
35. 26.23 Some Would Call It Hell; These Archaea Call It Home
35
Monday, November 26, 12
36. The Tree of Life
2006
36
adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
Monday, November 26, 12
37. The Tree of Life
2006
37
adapted from Baldauf, et al., in Assembling the Tree of Life, 2004
Monday, November 26, 12
38. Why tree useful?
• Reclassification of many organisms, including diversity of
pathogens
Changes how to design treatments
• Interpret comparative data
Convergence vs. homology
38
Monday, November 26, 12
39. Part II:
Genome Sequencing
39
Monday, November 26, 12
53. Microbial genomes
From http://genomesonline.org
Monday, November 26, 12
54. 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
• Comparative genomics
44
Monday, November 26, 12
56. Genome Sequences Have
Revolutionized Microbiology
• Predictions of metabolic processes
• Better vaccine and drug design
• New insights into mechanisms of evolution
• Genomes serve as template for functional
studies
• New enzymes and materials for engineering
and synthetic biology
Monday, November 26, 12
66. How to study microbes
• Key questions about microbes in environment:
Who are they? (i.e., what kinds of microbes are they)
What are they doing? (i.e., what functions and
processes do they possess)
56
Monday, November 26, 12
70. • For any particular environment, there are many different
ways one could go about characterizing the microbes there
• 1. Observe directly in the field
• 2. Grow in the laboratory
• 3. CSI Microbiology (collect & analyze DNA from field)
60
Monday, November 26, 12
71. A. Method 1
Method 1:
Observe in the field
61
Monday, November 26, 12
96. Examples of Benefits of Culturing:
• Allows one to connect processes and properties to single
types of organisms
• Enhances ability to do experiments from genetics, to
physiology to genomics
• Provides possibility of large volumes of uniform material for
study
• Can supplement appearance based classification with
other types of data. Many types are useful, though the
standard is analysis of rRNA sequences.
67
Monday, November 26, 12
98. Halophile adaptations
• Some stresses of high salt
Osmotic pressure on cells H20
Desiccation
69
Monday, November 26, 12
99. Halophile adaptations
• Some stresses of high salt
Osmotic pressure on cells H20
Desiccation
• Halophile adaptations
Increased osmolarity inside cell
Proteins H20
Carbohydrates
Salts
Membrane pumps
Desiccation resistance
70
Monday, November 26, 12
100. Halophile adaptations
• Some stresses of high salt
Osmotic pressure on cells
Desiccation
• Halophile adaptations
Increased osmolarity inside cell
Proteins
Carbohydrates
Salts - only done in extremely halophilic archaea
Membrane pumps
Desiccation resistance
71
Monday, November 26, 12
101. Halophile adaptations
• Some stresses of high salt
Osmotic pressure on cells
Desiccation
• Halophile adaptations
Increased osmolarity inside cell
Proteins
Carbohydrates
Salts - only done in extremely halophilic archaea
Membrane pumps
Desiccation resistance
High internal salt requires ALL cellular components to be
adapted to salt, charge. For example, all proteins must
change surface charge and other properties.
72
Monday, November 26, 12
103. Uses of extremophiles
Type of Examples Example of Practical Uses
environment mechanism of
survival
High temp Deep sea vents, Amino acid Heat stable enzymes
(thermophiles) hotsprings changes
Low temp Antarctic ocean, Antifreeze Enhancing cold
(psychrophile) glaciers proteins tolerance of crops
High pressure Deep sea vents, Solute changes Industrial processes
(barophile) hotsprings
High salt Evaporating pools Incr. internal Soy sauce production
(halophiles osmolarity
High pH Soda lakes Transporters Detergents
(alkaliphiles)
Low pH Mine tailings Transporters Bioremediation
(acidophiles)
Desiccation Deserts Spore formation Freeze-drying
(xerophiles) additives
High radiation Nuclear reactor Absorption, repair Bioremediation,
(radiophiles) waste sites damage space travel
74
Monday, November 26, 12
104. Method III:
CSI Microbiology
75
Monday, November 26, 12
105. Great Plate Count Anomaly
Culturing Microscopy
Count Count
76
Monday, November 26, 12
106. Great Plate Count Anomaly
Culturing Microscopy
Count <<<< Count
77
Monday, November 26, 12
107. Great Plate Count Anomaly
Problem because
appearance not
effective for “who
is out there?” or
“what are they
doing?”
Culturing Microscopy
Count <<<< Count
78
Monday, November 26, 12
108. Great Plate Count Anomaly
Solution?
Problem because
appearance not
effective for “who
is out there?” or
“what are they
doing?”
Culturing Microscopy
Count <<<< Count
79
Monday, November 26, 12
109. Great Plate Count Anomaly
Solution?
Problem because
appearance not
effective for “who
is out there?” or DNA
“what are they
doing?”
Culturing Microscopy
Count <<<< Count
80
Monday, November 26, 12
113. PCR and phylogenetic analysis of rRNA genes
DNA
extraction PCR
Makes lots of Sequence
PCR copies of the rRNA genes
rRNA genes
in sample
rRNA1
5’
...TACAGTATAGGTGG
Phylogenetic tree Sequence alignment = Data matrix AGCTAGCGATCGATC
GA... 3’
rRNA1 Yeast
rRNA1 A C A C A C
Yeast T A C A G T
E. coli A G A C A G
E. coli Humans Humans T A T A G T
83
Monday, November 26, 12
119. PCR and phylogenetic analysis of rRNA genes
DNA
extraction PCR
Makes lots of Sequence
PCR copies of the rRNA genes
rRNA genes
in sample
rRNA1
5’
...ACACACATAGGTG
Phylogenetic tree Sequence alignment = Data matrix GAGCTAGCGATCGAT
CGA... 3’
rRNA1 rRNA2
rRNA1 A C A C A C
rRNA2 T A C A G T rRNA2
5’
E. coli A G A C A G ...TACAGTATAGGTGG
E. coli Humans Humans T A T A G T AGCTAGCGATCGATC
GA... 3’
Yeast Yeast T A C A G T
88
Monday, November 26, 12
120. PCR and phylogenetic analysis of rRNA genes
DNA
extraction PCR
Makes lots of Sequence
PCR copies of the rRNA genes
rRNA genes
in sample
rRNA1
5’...ACACACATAGGTGGAGCTA
GCGATCGATCGA... 3’
Phylogenetic tree Sequence alignment = Data matrix
rRNA2
rRNA1 rRNA2
rRNA1 A C A C A C 5’..TACAGTATAGGTGGAGCTAG
CGACGATCGA... 3’
rRNA4
rRNA3 rRNA2 T A C A G T
rRNA3
rRNA3 C A C T G T 5’...ACGGCAAAATAGGTGGATT
E. coli Humans rRNA4 C A C A G T CTAGCGATATAGA... 3’
Yeast E. coli A G A C A G rRNA4
5’...ACGGCCCGATAGGTGGATT
Humans T A T A G T CTAGCGCCATAGA... 3’
Yeast T A C A G T
89
Monday, November 26, 12
121. Major phyla of bacteria and archaea (as of 2002)
No cultures
Some cultures
90
Monday, November 26, 12
122. Uses of rDNA PCR
Bohannan and
Hughes 2003
Hugenholtz 2002
91
Monday, November 26, 12
135. Glassy Winged Sharpshooter
• Feeds on xylem sap
• Vector for Pierce’s
Disease
• Potential bioterror agent
• Collaboration with Nancy
Moran to sequence
symbiont genomes
• Funded by NSF
• Published in PLOS
Biology 2006
Monday, November 26, 12
136. Wu et al. 2006 PLoS Biology 4: e188.
Monday, November 26, 12
137. Sharpshooter Shotgun Sequencing
shotgun
Collaboration with Nancy Moran’s
Wu et al. 2006 PLoS Biology 4: e188.
lab
Monday, November 26, 12