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
BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human ...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 11.
Symbioses and the Human MIcrobiome
Slides for Lectures by Jonathan Eisen
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
BIS2C. Biodiversity and the Tree of Life. 2014. L11. Symbioses and the Human ...Jonathan Eisen
BIS2C. Biodiversity and the Tree of Life.
At UC Davis Spring 2014.
Lecture 11.
Symbioses and the Human MIcrobiome
Slides for Lectures by Jonathan Eisen
4282020 Diamond Biology B - Spring -- Orange -- Quintero, Cr.docxtaishao1
4/28/2020 Diamond Biology B - Spring -- Orange -- Quintero, Crystal - Activities
https://isvaphs.agilixbuzz.com/student/128958493/activity/becbd6071e004cc69bc48560ac38af23 1/13
Bio U8 Practice Test 2 A
1.
2.
3.
Why is the shape of an enzyme important?
In secondary succession, what happens first?
A bird builds its nest in a tree. What type of relationship does the bird have with the tree?
The shape allows the reaction to go faster.
The shape allows the enzyme to make a new substrate.
The shape allows the enzyme to bind with a specific substrate.
The shape allows the enzyme to make products.
Wind brings lichens and mosses.
Small shrubs establish themselves.
Soil is built.
Grasses and other annual plants establish themselves.
symbiotic
commensalism
parasitism
mutualism
4/28/2020 Diamond Biology B - Spring -- Orange -- Quintero, Crystal - Activities
https://isvaphs.agilixbuzz.com/student/128958493/activity/becbd6071e004cc69bc48560ac38af23 2/13
4.
5.
6.
What is the name of the organization level missing from this picture?
A model of DNA is shown. What does the arrow indicate?
A snake with the genotype of TTPp mates with another snake with the genotype ttpp. What is the
probability that their offspring will have the genotype Ttpp?
cell
organelle
molecule
tissue
nucleotide
phosphate group
nucleic acid
deoxyribose sugar
75%
25%
50%
16.5%
4/28/2020 Diamond Biology B - Spring -- Orange -- Quintero, Crystal - Activities
https://isvaphs.agilixbuzz.com/student/128958493/activity/becbd6071e004cc69bc48560ac38af23 3/13
7.
8.
9.
10.
In order for complicated, self-replicating DNA to form, what do some scientists hypothesize
happened first?
Fungi in an ecosystem decompose matter. Why is this important?
Generally, the more genetic diversity a species has, the greater its chance for long-term survival.
This is due to which of the following?
Cars burn fossil fuels. How might this result in climate change?
Enzymes formed first.
Polymerization of amino acids happened in cold climates.
DNA formed as a result of natural selection.
RNA formed first.
Fungi return nitrogen and phosphorous into the soil that plant roots can absorb.
Fungi help produce atmospheric oxygen.
Fungi return glucose to the soil that plant roots can absorb.
Fungi help reduce atmospheric carbon dioxide.
Greater genetic diversity allows individuals to evolve.
Greater genetic diversity allows the strongest individuals to survive.
Greater genetic diversity allows populations to evolve.
Greater genetic diversity allows for more adaptations for changing environments.
Burning fossil fuels increases atmospheric carbon levels.
Burning fossil fuels decreases atmospheric nitrogen levels.
Burning fossil fuels decreases atmospheric carbon levels.
Burning fossil fuels increases atmospheric nitrogen levels.
4/28/2020 Diamond Biology B - Spring -- Orange -- Quintero, Crystal - Activities
https://isvaphs.agilixbuzz.com/student/128958493/activ.
Similar to BIS2C_2020. Lecture 8. Phylogenetic Diversity of Microbes (17)
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
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
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
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
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.
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.
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/
ANAMOLOUS SECONDARY GROWTH IN DICOT ROOTS.pptxRASHMI M G
Abnormal or anomalous secondary growth in plants. It defines secondary growth as an increase in plant girth due to vascular cambium or cork cambium. Anomalous secondary growth does not follow the normal pattern of a single vascular cambium producing xylem internally and phloem externally.
Deep Behavioral Phenotyping in Systems Neuroscience for Functional Atlasing a...Ana Luísa Pinho
Functional Magnetic Resonance Imaging (fMRI) provides means to characterize brain activations in response to behavior. However, cognitive neuroscience has been limited to group-level effects referring to the performance of specific tasks. To obtain the functional profile of elementary cognitive mechanisms, the combination of brain responses to many tasks is required. Yet, to date, both structural atlases and parcellation-based activations do not fully account for cognitive function and still present several limitations. Further, they do not adapt overall to individual characteristics. In this talk, I will give an account of deep-behavioral phenotyping strategies, namely data-driven methods in large task-fMRI datasets, to optimize functional brain-data collection and improve inference of effects-of-interest related to mental processes. Key to this approach is the employment of fast multi-functional paradigms rich on features that can be well parametrized and, consequently, facilitate the creation of psycho-physiological constructs to be modelled with imaging data. Particular emphasis will be given to music stimuli when studying high-order cognitive mechanisms, due to their ecological nature and quality to enable complex behavior compounded by discrete entities. I will also discuss how deep-behavioral phenotyping and individualized models applied to neuroimaging data can better account for the subject-specific organization of domain-general cognitive systems in the human brain. Finally, the accumulation of functional brain signatures brings the possibility to clarify relationships among tasks and create a univocal link between brain systems and mental functions through: (1) the development of ontologies proposing an organization of cognitive processes; and (2) brain-network taxonomies describing functional specialization. To this end, tools to improve commensurability in cognitive science are necessary, such as public repositories, ontology-based platforms and automated meta-analysis tools. I will thus discuss some brain-atlasing resources currently under development, and their applicability in cognitive as well as clinical neuroscience.
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 ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
Lateral Ventricles.pdf very easy good diagrams comprehensive
BIS2C_2020. Lecture 8. Phylogenetic Diversity of Microbes
1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BIS2C
Biodiversity & the Tree of Life
Spring 2020
Lecture 8:
Phylogenetic Diversity of Microbes
Prof. Jonathan Eisen
2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Anna’s Hummingbird in Davis, CA April 8, 2020
3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Learning Goals
1. Understand what type of data has been used to infer
the overall major structures in the Tree of Life
2. Understand the great plate count anomaly and how it
has impacted our view of the phylogenetic diversity of
life
3. Understand and be able to give examples of key
features present in key ancestors of major branches
in the tree of life (e.g., LUCA, BCA, ECA)
4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
!7: The Domains of Life
!8: Phylogenetic Diversity of Microbes
!9: Functional Diversity of Microbes
Lecture 8 Context
5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Lab Connections
• Lab 2 - Intro to Bacteria and Archaea
• Lab 2 - Station A - classification
• Lab 3 - Intro to microbial eukaryotes
• Lab 2 - Great plate count anomaly
8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Background: Review of Lecture 7
9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cell Structure Observations
L7: Prokaryotes vs. Eukaryotes
10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Mitochondria
Endoplasmic
Reticulum
Diploid
MeiosisBinary
Fission
Mitosis
Golgi
Linear DNACircular DNA
Haploid
Chromatin
12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
Interpreted as
implying this tree
because this would
require only one event
for the nucleus origin
13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
Interpreted as
implying this tree
because this would
require only one event
for the nucleus origin
14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
Interpreted as
implying this tree
because this would
require only one event
for the nucleus origin
15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
P1 P2 P3 E1 E2 E3P4
Prokaryotic
Eukaryotic
L7: Prokaryotes vs. Eukaryotes
Interpreted As Implying This Tree Because That Would
Require Only One Event For Nucleus Origin
But this is a mistake
since this tree, also
only requires one
event for origin of
the nucleus
16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotic
Eukaryotic
P1 P2 P3 E1 E2 E3P4
L7: Prokaryotes vs. Eukaryotes
So no reason to
assume this is the
correct tree, even
though many did
17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Woese rRNA Tree of Life
18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
L7: Woese rRNA Tree of Life
19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
P1 P2 P3 E1 E2 E3P4 P5 P6 P7
Prokaryotic
Eukaryotic
L7: Rooted Woese rRNA Tree of Life
20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 A3
Prokaryotic
Eukaryotic
L7: The Three Domain Tree of Life
EukaryaBacteria Archaea
Three Domains
Re-labelled
individual taxa
21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
L7: Loki’s Castle
• Loki’s Castle
22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Loki
Prokaryotic
Eukaryotic
EukaryaBacteria Archaea
Phylogenetic Trees
Using Genomes from
Lokiarchaea Look Like
This
L7: Alternative to Three Domain Tree of Life
23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Three Domain Tree of Life
Three Domain Tree of Life
Archaea Eukarya
Note Position of Asgard Archaea
New Slide
25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Method developments
!Same data, with different methods,
sometimes gives different results
!Some methods are more prone to artifacts
and errors than others
• Differences between genes
• Better taxonomic sampling
!Can improve resolution in trees
!Can help get around some method problems
Reasons for Changes in the Tree of Life
L7: Two Domain Tree of Life
26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
L7: Three Domain Tree of Life
Three Domain Tree of Life
Archaea Eukarya
Note Position of Asgard Archaea
New Slide
28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus tours
29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Key Lesson #1
• The overall structure of the tree of life has
been determined by analysis of molecular
sequence data
• Molecular data particularly important for
placing most microbes into the tree of life
31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Woese rRNA Tree of Life
32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Woese rRNA Tree of Life
33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
genome genomegenome
ACUGCACCUAU
CGUUCGACUGCACC
UAUCGUUCGACUGC
ACCUAUCGUUCGAC
UGCACCUAUCGUUC
GACCUAUCGUUCGA
CUGCACCUAUCGUU
CGACCUAUCGUUCG
ACUGCACCUAUCGU
UCG
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
CUAUCGUUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Woese rRNA Tree of Life
34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
B1 B2 B3 E1 E2 E3B4 A1 A2 Asgard
Prokaryotic
Eukaryotic
Bacteria
Two Domain Tree of Life
Two Domain Tree of Life
Archaea
Eukarya
“Prokaryotic
Archaea”
35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Two Domain Tree of Life
36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Two Domain Tree of Life
B1
B2
B3
E1
E2
E3
B4
A1
A2
Asgard
Bacteria
Archaea
Eukarya
“Prokaryotic
Archaea”
37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Two Domain Tree of
Life with Some Major
Subbranches Shown
38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Key Lesson #2
• Most microbes were only included in the tree
of life if they could be grown in the lab
39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
rRNA rRNArRNA
ACUGC
ACCUAU
CGUUCG
ACUCC
AGCUAU
CGAUCG
ACCCC
AGCUCU
CGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Woese rRNA Tree of Life
40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
<<<<
Culturing Observation
CountCount
42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Great Plate Count Anomaly
<<<<
Culturing Observation
CountCount
http://www.google.com/url?
sa=i&rct=j&q=&esrc=s&source=images&cd
=&docid=rLu5sL207WlE1M&tbnid=CRLQYP
7d9d_TcM:&ved=0CAUQjRw&url=http%3A%
2F%2Fwww.biol.unt.edu%2F~jajohnson%2F
DNA_sequencing_process&ei=hFu7U_TyCtO
qsQSu9YGwBg&psig=AFQjCNG-8EBdEljE7-
yHFG2KPuBZt8kIPw&ust=140487395121142
4
DNA
Lab 2:
“Culture Independent
DNA Studies”
43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Taxa Characters
S ACUGCACCUAUCGUUCG
R ACUCCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
F ACUCCAGGUAUCGAUCG
C ACCCCAGCUCUCGCUCG
W ACCCCAGCUCUGGCUCG
Taxa Characters
S ACUGCACCUAUCGUUCG
E ACUCCAGCUAUCGAUCG
C ACCCCAGCUCUCGCUCG
Environmental Sampling
genome genomegenome
ACUGCACCUAU
CGUUCGACUGCACC
UAUCGUUCGACUGC
ACCUAUCGUUCGAC
UGCACCUAUCGUUC
GACCUAUCGUUCGA
CUGCACCUAUCGUU
CGACCUAUCGUUCG
ACUGCACCUAUCGU
UCG
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
ACUGCACCUAU
CGUUCGACUGCACCU
AUCGUUCGACUGCAC
CUAUCGUUCGACUGC
ACCUAUCGUUCGACC
UAUCGUUCGACUGCA
CCUAUCGUUCGACCU
AUCGUUCGACUGCAC
CUAUCGUUCG
44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Same is true for
Archaea
47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Same is true for
Archaea
Also true for the
microbial lineages in
eukaryotes
48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Most of the
phylogenetic diversity
of bacteria only known
through DNA from
environmental
samples
Same is true for
Archaea
Also true for the
microbial lineages in
eukaryotes
No way to cover all
this diversity in this
class
49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Focus on this reduced
subset of the full
phylogenetic diversity
50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Plants: L14-21
Fungi L 22-23
Animals L 25-36
Choanos: L 24
Everything Else L 8-13
NOOP
Not Opisthokonts or Plants
Focus on this reduced
subset of the full
phylogenetic diversity
51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
L8: Features and
Innovations of Major
Groups
L9: Functional Diversity
L10: Parasites and
Pathogens
L11: Viruses and Gene
Transfer
L12: Mutualisms and
Microbiomes
L13: Endosymbioses and
Organelles
Everything Else L 8-13
NOOP
Not Opisthokonts or Plants
Focus on this reduced
subset of the full
phylogenetic diversity
52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
• Bonus Tours
54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
LUCA
LUCA
Last
Universal
Common
Ancestor
55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
LUCA
LUCA
Last
Universal
Common
Ancestor
Can infer
traits using
character
state
reconstruction
methods
57. • Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Universal Traits
58. • Made up of cells
• Use of DNA as a genetic material
• Use of ACTG in DNA
• Use of ACUG in RNA
• Three letter genetic code
• Central dogma (DNA » RNA » protein)
• Use water as a solvent
• Lipoprotein cell envelope
• 20 core amino acids in proteins
• Live on Earth
• Ribosome for translation
• RNA polymerase proteins
• Acquires energy from environment
• Store energy in chemicals
Universal Traits
Infer that
LUCA had all
of these
59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Mitochondria
Endoplasmic
Reticulum
Diploid
MeiosisBinary
Fission
Mitosis
Golgi
Linear DNACircular DNA
Haploid
Chromatin
61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Circular DNA
Linear DNA
62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Circular DNA
Linear DNA
63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Traits of LUCA = Last Universal Common Ancestor
• For characters that differ between prokaryotes
and eukaryotes, LUCA likely had the
character / character state found in
prokaryotes
!Circular DNA genome with plasmids
!No nucleus or membrane bound organelles
!Operons
!Binary fission reproduction
!Haploid
64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
!BCA
• Bonus Tours
65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
BCA
BCA
Bacterial
Common
Ancestor
66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
BCA = Bacterial Common Ancestor
• Likely inherited most of the traits inferred to
be in LUCA
• A few other key innovations, we are just going
to discuss one today
67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Peptidoglycan
• Unique to bacteria
• Polymer that provides a
firm, mesh like structure
around the cell
• Key component of cell
wall
• Is the target for many
antibiotics
68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Peptidoglycan
• Unique to bacteria
• Polymer that provides a
firm, mesh like structure
around the cell
• Key component of cell
wall
• Is the target for many
antibiotics
• Why?
69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
PG
Peptidoglycan
is a key
innovation of
bacteria
70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Peptidoglycan variation in bacteria
• Two major ways it is
used in bacteria
• Gram-positive bacteria -
thick peptidoglycan layer
outside 1 cell membrane
• Gram-negative bacteria
- thin peptidoglycan
layer outside between
two cell membranes
• This has many impacts
on biology, including
sensitivity to antibiotics
71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
!BCA
!ECA
• Bonus Tours
72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
ECA
Eukaryote
Common
Ancestor
73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Prokaryotes vs. Eukaryotes
EukaryotesProkaryotes
No Nucleus Nucleus
Two Main Kinds of Structures
What Other Differences Are There?
Mitochondria
Endoplasmic
Reticulum
Diploid
MeiosisBinary
Fission
Mitosis
Golgi
Linear DNACircular DNA
Haploid
Chromatin
75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
ECA
Eukaryote
Common
Ancestor
Tons of
innovations
thought to have
happened here
76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Many Other Innovations Associated w/ Origin of Euks
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
!LUCA
!BCA
!ECA
!Asgard Archaea and Eukaryotes
78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lokiarchaea named after Loki’s Castle Vent Site
79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Many Other Innovations Associated w/ Origin of Euks
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Found in Asgard Archaea
• Cell Structure
!Cytoskeleton
!Phagocytosis
!Diverse organelles and compartments
• Molecular Processes
!Mitosis (vs. binary fission)
!Sexual reproduction (vs. gene transfer)
" Meiosis
" Haploidy vs. Diploidy
" Fertilization
!Linear chromosomes & telomeres
!Chromosomes packaged into chromatin
!Decoupling of transcription and translation
!Introns and splicing
81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Some features
previously
thought to be
“Eukaryotic”
innovations
were likely
present in the
Eukaryote-
Asgard
ancestor
Cytoskeleton
Chromatin
84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Lecture 8 Outline
• Background and Context
• Phylogenetic Diversity of Life
• Features and Innovations of Major Groups
• Bonus Tours
85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Tour of Major Clades
• You Do Not Need to Know These Details
• Really
86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Bacteria
Tour
87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Spirochetes
• Gram-negative
• Motile
• Chemoheterotrophic
• Unique rotating, axial
filaments (modified flagella)
• Many are pathogens:
!Syphilis
!Lyme disease
• Others free-living
88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Chlamydias
• Gram-negative
• Cocci or rod-shaped
• Extremely small
• Live only as parasites
inside cells of
eukaryotes & cause
various diseases
!Trachoma
!Multiple sexually
transmitted diseases
!Pneumonia
C. trachomatis
89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Cyanobacteria
• Photolithoautotrophic
• Contain internal
membrane system
for photosynthesis
• Chloroplasts are
derived from
endosymbiotic
cyanobacteria
• Colonies can
differentiate into
vegetative cells,
spores, & heterocysts
90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Proteobacteria
• Gram-negative
• Escherichia coli: model
organism and human gut
commensal and
pathogen
• Mitochondria evolved
from this group
• Includes many human
and animal pathogens:
plague, cholera, typhoid
91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Low-GC Gram Positives (Firmicutes)
• Low G+C/A+T ratio in DNA
• Some produce endospores
which are resistant “seeds”
that germinate when
conditions are good
• Many agents of diseases
(e.g., anthrax, MRSA,
Streptococcus, botulism,
tetanus)
• Many of agricultural and
industrial use (e.g., Lactic
acid bacteria)
• Some (Mycoplasmas) have
no cell wall and are
extremely small
Mycoplasmas
92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
High-GC Gram Positives (Actinobacteria)
• High G+C/A+T ratio in DNA
• Elaborate branching
• Some reproduce by forming
chains of spores at tips of
filaments
• Most antibiotics are from
this group
• Causative agents of many
diseases such as
tuberculosis and leprosy
• Many originally misclassified
as fungi
93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Prokaryotic
Archaea
Tour
94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Crenarchaeota
• Most are both
thermophilic (heat
loving) & acidophilic
(acid-loving)
• Sulfolobus lives in
hot sulfur springs
(70–75°C, pH 2-3)
• One species of
Ferroplasma lives at
pH near 0
95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Euryarchaeota: Methanogens
• Only known methanogens
(produce methane (CH4)
by reducing CO2 ) - a form
of chemoautotrophy
• Methanogens release 2
billion tons of methane per
year
• Many live in the guts of
grazing mammals
• Many such as
Methanopyrus live in deep-
ocean hydrothermal vents
96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Euryarchaeota: Halophiles (Salt lovers)
• Pink carotenoid
pigments – very visible
• Have been found at
pH up to 11.5.
• Unusual adaptations
to high salt,
desiccation
• Many have
bacteriorhodopsin
which uses energy of
light to synthesize ATP
(photoheterotrophs)
97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
Amoebozoans
Excavates
Plantae
Rhizaria
Stramenopiles
Alveolates
Eukarya
Tour
98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae
The Plantae consist of
several clades; all
chloroplasts trace back to a
single incidence of
endosymbiosis.
99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Glaucophytes
• Unicellular, freshwater
organisms
• The chloroplast retains a bit
of peptidoglycan between the
inner and outer membrane.
100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Red Algae
• Most red algae are marine and
multicellular.
• Red pigment is phycoerythrin.
•Many reproduce with spores
Motile spores from
Purpureofilum
Audouinella pacifica
Spyridia
101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Chlorophytes
• Sister group to charophytes and land
plants.
• Synapomorphies include chlorophyll a
and b, and starch as a storage product.
• >17,000 species; marine, freshwater,
and terrestrial. Unicellular to large
multicellular forms.
Movement in the green alga
Volvox
Micrasterias
102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Plantae: Charophytes and Land Plants
STAY
TUNED
103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts
104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•Choanoflagellates are sister to the
animals.
•Some are colonial and resemble a type
of cell found in sponges.
The choanoflagellate Salpingoeca sp. feeding
Opisthokonts: Choanoflagellates
105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Opisthokonts: Fungi and Animals
STAY
TUNED
106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates
Alveolates
Have alveoli or
sacs beneath
surface of
plasma
membrane.
All are unicellular;
many are
photosynthetic.
107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•Most are marine and are important photoautotrophic
primary producers
•Mixture of pigments give them a golden brown color.
•Have two flagella, one in an equatorial groove, the other
in a longitudinal groove.
Alveolates: Dinoflagellates
Certium
tenue
Coral symbiont
108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Apicomplexans
• All parasitic
• Have a mass of organelles at one tip—the
apical complex that help the parasite enter
the host’s cells.
Apical complex • Plasmodium falciparum-
Malaria kills 700,000-2,000,000
people per year—75% of them
are African children
109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Alveolates: Ciliates
Movement in a ciliate from the gut of a termite
• All have numerous cilia, the structure is
identical to flagella.
• Most are heterotrophic; very diverse group.
• Have complex body forms and two types of
nuclei.
110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles
Stramenopiles
Two flagella, with rows of tubular hairs
on the longer one.
111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
•All are multicellular; some get very large (e.g., giant
kelp).
•The carotenoid fucoxanthin imparts the brown color.
•Almost exclusively marine.
Stramenopiles: Brown Algae
A community of brown algae: The marine kelp forest
112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Diatoms
A colony of the diatom, Bacillaria
paradoxa
•Unicellular, but many associate in filaments.
•Have carotenoids and appear yellow or
brown.
•Excellent fossil record
•Most are photoautotrophic
•Responsible for 20% of all carbon fixation.
•Oil, gas source
113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Stramenopiles: Oomcyetes
Phytophthora
Potato Late Blight
• Non-photosynthetic.
• Are absorptive heterotrophs
• Once were classed as fungi, but are
unrelated.
Sudden Oak Death
114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizaria
Rhizaria
Unicellular, aquatic, with long, thin pseudopods.
115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizaria: Cercozoans
Some cercozoans are aquatic, others live
in soil.
They have diverse forms and habitats.
One group has chloroplasts derived from a
green alga by secondary endosymbiosis.
Euglyphid
Chlorarachnion reptans
116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizaria: Foraminiferans
Sand beaches in the tropics
• Secrete shells of calcium carbonate.
• Discarded shells make up limestone.
• Create some beach sands
• Used to date & characterize sedimentary
rocks.
• Some live as plankton, others at sea bottom.
• Thread-like, branched pseudopods extend
through pores in the shell and form a sticky net
that captures smaller plankton.
117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Rhizaria: Radiolarians
• Have thin, stiff pseudopods reinforced
by microtubules.
• The pseudopods increase surface
area for exchange of materials; and
help the cell float.
• Exclusively marine, most secrete
glassy endoskeletons, many with
elaborate designs.
119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Diplomonads and Parabisalids
• Unicellular
• Lack mitochondria and most are
anaerobic. This is a derived condition
• Giardia lamblia - a diplomonad - is a
human parasite
• Trichomonas vaginalis - parabasalid - STD
120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Heteroloboseans
• Amoeboid body form.
• Naegleria can enter humans and
cause a fatal nervous system
disease - “brain eating”
• Some can transform between
amoeboid and flagellated stages.
121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Euglenids
• Have flagella.
• Some are
photosynthetic,
some always
heterotrophic, and
some can switch.
Movement in the euglenoid Eutreptia
122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Excavates: Kinetoplastids
• Unicellular parasites with two flagella and a
single mitochondrion.
• Mitochondrion contains a kinetoplast -
structure with multiple, circular DNA
molecules
• Includes trypanosomes and agents of
chagas, sleeping sickness, Leishmaniasis
Trypanosoma sp.
mixed with blood cells
123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Amoebozoans
Amoebozoans
Lobe-shaped pseudopods are used for
locomotion.
124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
• Not colonial; live as single cells
• Some secrete shells or glue sand
grains together to form a casing.
• Many pathogens
Amoebozoans: Loboseans
125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Entamoeba histolytica
http://www.npr.org/blogs/health/2014/04/09/300991364/gut-eating-amoeba-
caught-on-film
126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Amoebozoans: Plasmodial Slime Molds
• Individual motile cells can form single,
multinucleate cell (plasmodium)
• Ingest food by endocytosis
• Form spores on stalks called fruiting
bodies.
• Found in cool, moist habitats
127. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
Amoebozoans: Cellular Slime Molds
• Life cycle consists of individual motile cells that
ingest food by endocytosis
• This is followed by the formation of single,
multicellular fruiting structure
• Each cell retains its own plasma membrane and
individuality
Karyog
128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
End of The Tours
• End of the Tours
129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2020
!7: The Domains of Life
!8: Phylogenetic Diversity of Microbes
!9: Functional Diversity of Microbes
Lecture 8 Context
• See you Monday for Functional Diversity of
Microbes