Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles.
2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species.
3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria).
Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the microbial diversity of permafrost. Explain how the greatest diversity of Archaea exist in cold environments.
2. Describe the two main Archaeal phyla, and describe example species.
3. Explain how climate change is affecting permafrost and microbial diversity.
Unit 8: Rare and Uncultured Microbes
LECTURE LEARNING GOALS
1. Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes.
2. Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life.
3. For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated.
6
Unit 4: Biofilms & Motility
LECTURE LEARNING GOALS
• Describethethreetypesofbacterialbiofilm, and how each develop.
• Contrastthedifferentwaysthatmicrobes move using flagella. Explain the ways that bacterial and archaeal flagella are different. Describe non-flagellar movement.
• Giveexamplesofhowmicrobesmovefrom the phyla spirochetes and bacteroidetes.
Unit 5: Everything is everywhere?
LECTURE LEARNING GOALS
1. State the Baas Becking hypothesis, and describe the environmental traits are the strongest drivers of microbial community.
2. Explain how to measure community dissimilarity. Explain why the Baas Becking hypothesis continues to be tested today.
3. Describe methods to link taxonomic or community structure to function.
Unit 9: Human Microbiome
LECTURE LEARNING GOALS
1. Describe the human microbiome: how many microbes there are, how you get your microbiome, who’s there, and how it changes over time and by region.
2. Describe the domain eukarya. List the five superkingdoms and a few notable species.
3. Explain how the human microbiome is related to health and disease.
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?
Unit 6: Diversity of Microbial Mats
LECTURE LEARNING GOALS
1. Definemicrobialmats.Describethe functional guilds of microbes in the different layers, and how they interact.
2. Foreachofthethreephylaof photosynthetic bacteria, contrast how each fixes C and gains energy and reducing equivalents from light.
3. Forthetwothermophilicbacterialphyla, describe their adaptations to life at high
temperature. Explain how they are primitive and deeply-branching.
Unit 7: Diversity of Soils & Sediments
LECTURE LEARNING GOALS
1. Define soils and sediment, and contrast the microbes living in each. Explain biogeochemical cycles.
2. Describe the diversity, metabolism & habitat of the five classes of the phylum Proteobacteria, including some common example species.
3. Describe the diversity, metabolism & habitat of the Gram-positive bacteria (phylua Firmicutes & Actinobacteria).
Unit 10: Diversity of Permafrost
LECTURE LEARNING GOALS
1. Describe permafrost, and the microbial diversity of permafrost. Explain how the greatest diversity of Archaea exist in cold environments.
2. Describe the two main Archaeal phyla, and describe example species.
3. Explain how climate change is affecting permafrost and microbial diversity.
Unit 8: Rare and Uncultured Microbes
LECTURE LEARNING GOALS
1. Describe the phyla containing rare bacteria: Deinococcus/Thermus, Chlamydia & Planctomycetes.
2. Describe the sequencing methods used to understand uncultured microbes. Explain the Eocyte hypothesis and how this model differs from the three domain tree of life.
3. For the cultured microbes, describe major characteristics for the 13 bacterial phyla, and explain why some microbe remain uncultivated.
6
Unit 4: Biofilms & Motility
LECTURE LEARNING GOALS
• Describethethreetypesofbacterialbiofilm, and how each develop.
• Contrastthedifferentwaysthatmicrobes move using flagella. Explain the ways that bacterial and archaeal flagella are different. Describe non-flagellar movement.
• Giveexamplesofhowmicrobesmovefrom the phyla spirochetes and bacteroidetes.
Unit 5: Everything is everywhere?
LECTURE LEARNING GOALS
1. State the Baas Becking hypothesis, and describe the environmental traits are the strongest drivers of microbial community.
2. Explain how to measure community dissimilarity. Explain why the Baas Becking hypothesis continues to be tested today.
3. Describe methods to link taxonomic or community structure to function.
Unit 9: Human Microbiome
LECTURE LEARNING GOALS
1. Describe the human microbiome: how many microbes there are, how you get your microbiome, who’s there, and how it changes over time and by region.
2. Describe the domain eukarya. List the five superkingdoms and a few notable species.
3. Explain how the human microbiome is related to health and disease.
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?
Unit 6: Diversity of Microbial Mats
LECTURE LEARNING GOALS
1. Definemicrobialmats.Describethe functional guilds of microbes in the different layers, and how they interact.
2. Foreachofthethreephylaof photosynthetic bacteria, contrast how each fixes C and gains energy and reducing equivalents from light.
3. Forthetwothermophilicbacterialphyla, describe their adaptations to life at high
temperature. Explain how they are primitive and deeply-branching.
Kingdom Monera
Bacteria
structure of Bacteria
shapes of Bacteria
reproduction in bacteria
How do Bacteria cause disease?
How can Bacteria work to our benefit?
CYNOBACTERIA
Example of cynobacteria
Cyanobacteria terminology
Actinomycetes
Streptomyces
Functions/Role of actinomycetes
Evolution Of Bacteria
Bacteria have existed from very early in the history of life on Earth. Bacteria fossils discovered in rocks date from at least the Devonian Period (419.2 million to 358.9 million years ago), and there are convincing arguments that bacteria have been present since early Precambrian time, about 3.5 billion years ago. Bacteria were widespread on Earth at least since the latter part of the Paleoproterozoic, roughly 1.8 billion years ago, when oxygen appeared in the atmosphere as a result of the action of the cyanobacteria. Bacteria have thus had plenty of time to adapt to their environments and to have given rise to numerous descendant forms.
Bacteria are microscopic, single-celled organisms that thrive in diverse environments. These organisms can live in soil, the ocean and inside the human gut. Humans' relationship with bacteria is complex. Sometimes bacteria lend us a helping hand, such as by curdling milk into yogurt or helping with our digestion
1.1 The Beginnings of Microbiology1. • The discovery of mic.docxjoyjonna282
1.1 The Beginnings of Microbiology
1. • The discovery of microorganisms
was dependent on observations made with
the microscope
2. • The emergence of experimental
science provided a means to test long held
beliefs and resolve controversies
3. MicroInquiry 1: Experimentation and
Scientifi c Inquiry
1.2 Microorganisms and Disease Transmission
4. • Early epidemiology studies
suggested how diseases could be spread and
be controlled
5. • Resistance to a disease can come
from exposure to and recovery from a mild
form of (or a very similar) disease
1.3 The Classical Golden Age of Microbiology
6. (1854-1914)
7. • The germ theory was based on the
observations that different microorganisms
have distinctive and specifi c roles in nature
8. • Antisepsis and identifi cation of the
cause of animal diseases reinforced the germ
theory
9. • Koch's postulates provided a way to
identify a specifi c microorganism as causing a
specifi c infectious disease
10. • Laboratory science and teamwork
stimulated the discovery of additional
infectious disease agents
11. • Viruses also can cause disease
12. • Many benefi cial bacteria recycle
nutrients in the environment
Cell Structure
and Function
in the Bacteria
and Archaea
4
Our planet has always been in the “Age of Bacteria,” ever since the first
fossils—bacteria of course—were entombed in rocks more than 3 billion
years ago. On any possible, reasonable criterion, bacteria are—and always
have been—the dominant forms of life on Earth.
—Paleontologist Stephen J. Gould (1941–2002)
97
Chapter Preview and Key Concepts
“Double, double toil and trouble; Fire burn, and cauldron bubble” is the
refrain repeated several times by the chanting witches in Shakespeare’s
Macbeth (Act IV, Scene 1). This image of a hot, boiling cauldron actu-
ally describes the environment in which many bacterial, and especially
archaeal, species happily grow! For example, some species can be iso-
lated from hot springs or the hot, acidic mud pits of volcanic vents
( FIGURE 4.1 ).
When the eminent evolutionary biologist and geologist Stephen J. Gould
wrote the opening quote of this chapter, he as well as most microbiologists
had no idea that embedded in these “bacteria” was another whole domain
of organisms. Thanks to the pioneering studies of Carl Woese and his col-
leagues, it now is quite evident there are two distinctly different groups of
“prokaryotes”—the Bacteria and the Archaea (see Chapter 3). Many of the
organisms Woese and others studied are organisms that would live a happy
life in a witch’s cauldron because they can grow at high temperatures, produce
methane gas, or survive in extremely acidic and hot environments—a real
cauldron! Termed extremophiles, these members of the domains Bacteria
4.1 Diversity among the Bacteria and Archaea
1. The Bacteria are classified into several
major phyla.
2. The Archaea are currently classified into two
major phyla.
4.2 Cell Shapes and Arran ...
Kingdom Monera
Bacteria
structure of Bacteria
shapes of Bacteria
reproduction in bacteria
How do Bacteria cause disease?
How can Bacteria work to our benefit?
CYNOBACTERIA
Example of cynobacteria
Cyanobacteria terminology
Actinomycetes
Streptomyces
Functions/Role of actinomycetes
Evolution Of Bacteria
Bacteria have existed from very early in the history of life on Earth. Bacteria fossils discovered in rocks date from at least the Devonian Period (419.2 million to 358.9 million years ago), and there are convincing arguments that bacteria have been present since early Precambrian time, about 3.5 billion years ago. Bacteria were widespread on Earth at least since the latter part of the Paleoproterozoic, roughly 1.8 billion years ago, when oxygen appeared in the atmosphere as a result of the action of the cyanobacteria. Bacteria have thus had plenty of time to adapt to their environments and to have given rise to numerous descendant forms.
Bacteria are microscopic, single-celled organisms that thrive in diverse environments. These organisms can live in soil, the ocean and inside the human gut. Humans' relationship with bacteria is complex. Sometimes bacteria lend us a helping hand, such as by curdling milk into yogurt or helping with our digestion
1.1 The Beginnings of Microbiology1. • The discovery of mic.docxjoyjonna282
1.1 The Beginnings of Microbiology
1. • The discovery of microorganisms
was dependent on observations made with
the microscope
2. • The emergence of experimental
science provided a means to test long held
beliefs and resolve controversies
3. MicroInquiry 1: Experimentation and
Scientifi c Inquiry
1.2 Microorganisms and Disease Transmission
4. • Early epidemiology studies
suggested how diseases could be spread and
be controlled
5. • Resistance to a disease can come
from exposure to and recovery from a mild
form of (or a very similar) disease
1.3 The Classical Golden Age of Microbiology
6. (1854-1914)
7. • The germ theory was based on the
observations that different microorganisms
have distinctive and specifi c roles in nature
8. • Antisepsis and identifi cation of the
cause of animal diseases reinforced the germ
theory
9. • Koch's postulates provided a way to
identify a specifi c microorganism as causing a
specifi c infectious disease
10. • Laboratory science and teamwork
stimulated the discovery of additional
infectious disease agents
11. • Viruses also can cause disease
12. • Many benefi cial bacteria recycle
nutrients in the environment
Cell Structure
and Function
in the Bacteria
and Archaea
4
Our planet has always been in the “Age of Bacteria,” ever since the first
fossils—bacteria of course—were entombed in rocks more than 3 billion
years ago. On any possible, reasonable criterion, bacteria are—and always
have been—the dominant forms of life on Earth.
—Paleontologist Stephen J. Gould (1941–2002)
97
Chapter Preview and Key Concepts
“Double, double toil and trouble; Fire burn, and cauldron bubble” is the
refrain repeated several times by the chanting witches in Shakespeare’s
Macbeth (Act IV, Scene 1). This image of a hot, boiling cauldron actu-
ally describes the environment in which many bacterial, and especially
archaeal, species happily grow! For example, some species can be iso-
lated from hot springs or the hot, acidic mud pits of volcanic vents
( FIGURE 4.1 ).
When the eminent evolutionary biologist and geologist Stephen J. Gould
wrote the opening quote of this chapter, he as well as most microbiologists
had no idea that embedded in these “bacteria” was another whole domain
of organisms. Thanks to the pioneering studies of Carl Woese and his col-
leagues, it now is quite evident there are two distinctly different groups of
“prokaryotes”—the Bacteria and the Archaea (see Chapter 3). Many of the
organisms Woese and others studied are organisms that would live a happy
life in a witch’s cauldron because they can grow at high temperatures, produce
methane gas, or survive in extremely acidic and hot environments—a real
cauldron! Termed extremophiles, these members of the domains Bacteria
4.1 Diversity among the Bacteria and Archaea
1. The Bacteria are classified into several
major phyla.
2. The Archaea are currently classified into two
major phyla.
4.2 Cell Shapes and Arran ...
Unit 3: Microbiology of Early Earth
LECTURE LEARNING GOALS
• Describe the early Earth environment, and prevailing theories for the origins of life.
• Describe the major events in the evolution of cellular life, and when they happened.
• Explain the lines of evidence that lead us to know when early life arose, and the scientific basis behind each line.
La botánica (del griego βοτάνη, 'hierba') o fitología (del griego φυτόν, 'planta' y λόγος, 'tratado') es la rama de la biología que estudia las plantas bajo todos sus aspectos, incluyendo la descripción, clasificación, distribución, identificación, estudio de la reproducción, fisiología, morfología, relaciones recíprocas, relaciones con los otros seres vivos y efectos provocados sobre el medio en el que se encuentran.
Instructions and bracket to play Morrill Microbe Madness, a game to review representative organisms from the major phyla of the domain bacteria, part of MICROBIO 480 Microbial Diversity.
Unit 11: Viruses and Prions
LECTURE LEARNING GOALS
1. Define what is a virus, and describe the three theories on the origin of viruses.
2. Define and contrast prions and subviral agents. Explain how they are different from viruses.
3. Explain coronaviruses, the origin of SARS- CoV-2, how it infects cells, and the tools we use to fight the spread of COVID-19.
Unit 2: Phylogeny
LECTURE LEARNING GOALS
1. Define phylogeny, and describe what a phylogenetic tree can reveal about the species it models.
2. Describe how to construct a phylogenetic tree, and the complexities that create mistakes.
3. Explain how to root a tree, and contrast how to root the tree of life.
Learning Objectives:
1. Describe the 8-week CIRTL MOOC, An Introduction to Evidence-Based Undergraduate STEM Teaching.
2. Identify some tools that you can use to improve STEM learning outcomes for undergraduate students.
3. Feel enabled to incorporate one or two new ideas into your teaching.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
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.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Richard's entangled aventures in wonderlandRichard 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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
1. Key for activity reviews in
class
Microbiology 480
Microbial Diversity
Spring 2018
2. KEY: Activity for Review of
Unit 01.1 Founders of Microbiology
1. Visualizing microbes
a. Antonie van Leeouwenhoek
b. As a lens grinder, made the first microscope thus the first observation of
microbes
2. Sterile technique
a. Louis Pasteur
b. Using the swan-necked flasks, developed “pasterurization” as a way to sterilize
media, the first controlled cultivation
3. Culturing single colonies
a. Robert Koch
b. With his assistant Julius Richard Petri, developed agar plates for isolating single
colonies, or cultures derived from single cells, the first isolation of microbes
4. Method for defining causative agents
a. Robert Koch
b. Developed “Koch’s postulates” as a way of showing causation of disease-causing
mirobes, but process is often applied to other scenarios
5. Sequencing methods for true phylogenies
a. Carl Woese
b. Developed primers for PCR Sanger sequencing of the small subunit ribosomal
RNA gene, which revealed the very divergent new (at the time) domain Archaea
3. KEY: Activity for Review of
Unit 01.2 Measures of Diversity
Draw a picture of the Woesian Tree of Life, and
annotate it with labels including
a. The contribution of Carl Woese – 3 domains of life
b. The contribution of Ernst Haeckl – archaea +
bacteria = protista or prokaryotes
c. The contribution of Carl Linnaeus - DKPCOFGS
Bacteria
Archaea
Eukaryotes
4. KEY: Activity for Review of
Unit 01.3 Extent of Diversity
For each set of pairs, which environment has the
most microbes? Which has the most diversity? Why?
1. Salt marsh likely has more micorbes than the open ocean because there
is more food (from plant root exudates and decomposing plant litter). For
this reason, there is likely to be more diversity in the salt marsh, too, because
there is more diversity in niches: food source, aerobic and anaerobic
environments, surface and free-living spaces.
2. Top, surface soil will have more microbes than deep soil, because there is
more food (from soil organic matter, plant root exudates and plant litter).
Deep soil might have similar diversity because both environments have a
range of niches, but deep soil has more minerals and more anaerobic sites.
3. The gut has almost all of the microbes in the human microbiome, so this
site will certainly have more microbes compared to skin. But because of
the diversity of niches in skin, the diversity of the microbes there might be
comparable. It likely depends on the host’s diet health.
5. KEY: Activity for Review of
Unit 02.1 Reading Trees
1. Circle the groups included in the Prokaryotes.
2. The group Prokaryote is
a. Monophyletic – all have a common ancestor.
b. Polyphyletic – species have many common ancestors.
c. Paraphyletic - group excludes one ancestor.
The
term
prokaryote
defines
organisms
by
what
do
not
have
(nuclei).
It
is
be=er
not
to
measure
organisms
by
their
form
or
func?on,
because
these
traits
can
be
plas?c
(changing).
Nuclei
are
not
an
ancestral
trait.
6. KEY: Activity for Review of
Unit 02.2 Making Trees
1. Which tree is a more likely
representation of
Methanopyrus kandleri?
Why?
The top tree, because the branche
for M. kandleri have higher
bootstrap values
2. What could explain the
differences between the
two trees?
Perhaps one of the genes was
horizontally transferred, meaning
that it is not a true phylogeny.
One gene could be under selective
pressure or could have a different
function in one set of organisms
compared to the others.
7. KEY: Activity for Review of
Unit 02.3 Rooting Trees
• What can we infer about the biology of the Last
Universal Common Ancestor based on the fact that
different genes place the root in different Domains?
– LUCA had characteristics of both Bacteria and Archaea
– Because DNA sequence-related genes puts the root
within the Bacteria, the LUCA likely had DNA-based
functions (replication, for example, elongation factors)
more like modern day Bacteria
– LUCA will share other characteristics with bacteria that
root the tree this way, e.g., ATPases
– Because protein sequence puts the root of the tree of
life within the Archaea, the LUCA likely had proteins
that looked more like Archaea
– Same is true for tRNA, 5S, Rnase P: LUCA would have
looked more like Archaea
8. KEY: Activity for Review of
Unit 03.1 Early Earth
• Place the following events in the history of Earth in order:
__3__ First eukaryotes with endosymbiotic Rickettsiales (first
mitochondria)
__2__ First plants with endosymbiotic cyanobacteria (first chloroplasts)
__1__ First eukaryotes
__4__ First land plants
• First plants would have to come before first land plants
• Plants are eukaryotes with chloroplasts, so first eukaryotes would
have to come before plants or land plants
• 2.5 Ga – First eukaryotes (cells with nucleus)
• 1.5 Ga – First eukaryotes with endosymbiotic Rickettsiales (Sar11
clade) bacteria, now mitochondria: symbiogenesis
• 1.5-1 Ga – First plants with endosymbiotic cyanobacteria
(chloroplasts)
• ~475 Ma – first land plants
9. KEY: Activity for Review of
Unit 03.2 Evolution of Cellular Life
• What were some characteristics of protocells? In answering,
describe if it had:
– DNA – no, DNA was the last biomolecule to evolve
– RNA – yes, would have had RNA acting catalytically as well as
encoding some functions
– Lipids – almost certainly; lipid sacs called micelles form
naturally
– Membranes – we assume there was a membrane bilayer with
proteins in the membrane
– Proteins – no, because the presence of proteins is the mark of
a cell, used for metabolism and import into the cell
– Replication – yes, even early protocells “replicated” as they
travelled currents from warm to cool
• Was LUCA a protocell? Why or why not? – the last
protocell would have been separated from LUCA by up to a
billion years (4Ga for first life, 3Ga for first “prokaryote”, or
LUCA).
10. KEY: Activity for Review of
Unit 03.3 Evidence for Early Life
How do we know that the first life on Earth occurred about
3.5 Ga?
• Old rock deposits are identified by radiogenic dating. Once
they are identified as very Old Rock (over 3 Ga), isotopic
fractionation can be used to show that the carbon in the
rock is organic.
• Microfossils may be found in old rock deposits identified by
radiogenic dating. Once they are identified as very Old Rock
(over 3 Ga), isotopic fractionation shows that the
microfossils are organic and thus microbial cells.
• Some lipids or other complex molecules are only found in
microbes. If these are found in Old Rock, this can be used
to date early life.
• Phylogenetic trees can act as molecular clocks. A good tree
can be used to root the tree of life and estimate the age
of early life, based on assumptions about the rate of
mutation (a proxy for the rate of evolution).
11. KEY: Activity for Review of
Unit 04.1 Biofilms
Draw a picture of how a biofilm “cycles” as a form of
dispersing. Include in your diagram labels for the five
stages of biofilm growth.
1. Initial attachment,
2. Irreversible attachment,
3. Maturation,
4. Recruitment, and
5. Dispersion.
1
2
3
4
5
12. KEY: Activity for Review of
Unit 04.2 Motility
We discussed four types of flagellar arrangements earlier. What
type do you think spirochaetes have, and why?
• The four types are
A. Monotrichous bacteria have a single flagellum (e.g., Vibrio
cholerae).
B. Lophotrichous bacteria have multiple flagella located at the
same spot on the bacteria's surfaces which act in concert to
drive the bacteria in a single direction.
C. Amphitrichous bacteria have a single flagellum on each of two
opposite ends (only one flagellum operates at a time, allowing
the bacteria to reverse course rapidly by switching which
flagellum is active).
D. Peritrichous bacteria have flagella projecting in all directions
(e.g., E. coli).
Spirochaetes can be monotrichous, lophotrichous or amphitrichous.
The important characteristics are that (1) the flagella does not
emerge from the outer membrane, and (2) is located only at one or
both ends
13. KEY: Activity for Review of
Unit 04.3 Managing Movement
• Which statements are true about quorum
sensing? (Circle all that apply.)
a. Quorum sensing enables bacteria to co-
ordinate their behavior. YES.
b. The QS signal is constitutively produced at
a low levels. YES.
c. Quorum sensing genes always occur in
pairs of synthase and receptor genes. YES.
d. Different QS signals may elicit different
behaviors. YES.
14. KEY: Activity for Review of
Unit 05.1 Geographic distance
This is an aerial photo of the Don Juan Pond in
Antarctica has 40% salinity; this is the saltiest known
body of water on Earth.
1. This is a C-limiting environment. What kind of
compatable solutes do microbes make here?
– A microbe experiencing osmotic stress in conditions
where carbon is limiting will likely make compatible
solutes that are non-carbon based. This should include
Phosphorous (K+) and Sodium (Na+).
2. Would you expect this environment to have high or
low diversity? Why?
– This environment should be low in diversity, because
salinity is the strongest driver of microbial community
structure, and special funcitons are required for living
in high salinity environments.
15. KEY: Activity for Review of
Unit 05.2 Community distance
Some marine bacteria display bipolar distributions in the
Earth's oceans, occurring exclusively at the north and south
poles and nowhere else. Is this evidence for or against the
Baas-Becking Hypothesis? Explain, and be sure to restate the
Baas-Becking Hypothesis.
• This observation is evidence for the Baas-Becking
Hypothesis, which is that “everything is everywhere but the
environment selects.”
• If everything were everywhere, then it all types of
organisms are present at even very small abundances in all
environments. If the environment selects, then this bipolar
distribution (evident only at the two poles) might suggest
that there is something special about the poles that
encourages the growth of the marine bacteria.
16. KEY: Activity for Review of
Unit 05.3 Linking function to phylogeny
If you wanted a measure of microbial functions in a natural
environment, which method of sequencing would be
appropriate? Circle all that apply.
• Comparative genomics – NO, this measure of sequencing genomes of
isolated organisms cannot now be done in mixed, natural communities
• Metagenomics – YES, sequencing all the DNA from a mixed community
will give you an estimate of possible functions
• Metatranscriptomics – YES, also called RNAseq, this sequencing of all
RNA is a measure of genes transcribed
• Phylogenetics – NO, this measure of gene markers of evolution only
gives information on function by proxy and is not a direct measure of
microbial function
• Stable isotope probing – YES, perhaps the best measure of microbial
function, if the substrate for the funciton of interest can be added as
an isotopically labeled substrate
17. KEY: Activity for Review of
Unit 06.1
• Draw a photosynthetic microbial mat, and map out the layers to
show how the primary producers at the top indirectly provide
energy and carbon to the organisms at the bottom.
Top green layers = green algae, cyanobacteria
- fix C, exude sugars that may be available to lower layers
Pink layer = purple sulfur bacteria
- anoxygenic phototrophs, oxidize H2S to S or SO4 for energy
Orange layer = spirochaetes
- microaerophilic heterotrophs
Purple layer = green sulfur bacteria
- photosynthetic, oxidize sulfide for reducing equivlaents
Black layer = sulfate reducers
- reduce SO4 to H2S obtained from upper layers
Bottom is iron sulfide-rich waste products and decaying mats
18. KEY: Activity for Review of
Unit 06.2
1. Chloroplasts are derived from an ancient
endosymbiotic event, and belong to the
Phylum Cyanobacteria (blue-green algae).
2. Like the cyanobacteria, they fix carbon via
the calvin cycle, and make reducing
equivalents and energy (ATP) from light using
oxygenic photosynthesis, which employs the
two photosystem, Z-scheme of electron
transport from the reaction center, to
chlorophyll a to the FeS center to the
electron transport chain.
19. KEY: Activity for Review of
Unit 06.3
• The Aquificae and Thermotogae are both primitive and deep-
branching phyla. Can you draw a tree with deep branches that
are not primitive, and with primitive branches that are not deep?
Do you know of any examples of either?
• A great example of deep, long branches is the eukaryotic tree, in
which the deep branches are long (and mostly parasitic) and the
plants and animals are relatively short branches. An open question
in evolution is: what exactly IS a “deep” branch? If you add a
large collection of sequences to the Thermotoga lineage (say, all
known species in this group) and prune many of the sequences
from the rest of the tree, only the Aquificae branches look “deep”
now. Primitive species have short branch lengths, so are more
closely related to the common ancestor. Deep branches have
direct lineages closer to the root of the Tree of Life. An organism
can be deeply rooted, or primitive, or both.
20. KEY: Activity for Review of
Unit 07.1
• How are soil and sediment related?
– Sediment is soil moved by water.
• What is the name for soil influenced by
plant roots? Rhizosphere soil.
• Why are the acid-rich sediments of the Rio
Tinto considered analog sites for studying
possible life on Mars?
– Due to a mining accident, the Rio Tinto is replete
with heavy metals and iron. Anoxic conditions in
the sediment replicate anoxic environments on
Mars. Because there seems to have been water
on Mars in the past, the Rio Tinto could look like
Martian sediment from past eons.
21. KEY: Activity for Review of
Unit 07.2
• What microbe is an environmental biocontrol
agent for mosquito-transmitted viral
pathogens? Wolbachia, an Alphaproteobacteria
• What microbe is the ancestor of the
mitochondria? Rickettsia, an
Alphaproteobacteria
• What microbe is responsible for ulcers?
Helicobacter pylori, an Epsilonproteobacteria
• What phylum and class do the purple sulfur
bacteria belong to? The Gammaproteobacteria,
for example Chromatium spp.
22. KEY: Activity for Review of
Unit 07.3
• For each microbe listed, name the phylum
it belongs to, and match it to its
function.
_ Bacillus cereus - Soil microbe that produces
endospores
_ Mycobacterium tuberculosis - Animal
pathogen with no known environmental
reservoir
_ Streptomyces antibioticus - Most common
source of industrial antibiotics
23. KEY: Activity for Review of
Unit 08.1
Match the rare phylum-associated bacteria with its relatively
unique morphology. Taxa may be used more than once.
1. Elemental bodies - B
2. Extreme tolerance to UV irradiation - D
3. Pirrelulosomes – A
4. Riboplasm - A
5. Taq polymerase - C
6. Division by septal curtain - D
a) Blastopirellula marina
b) Chlamydia
c) Thermus aquaticus
d) Deinoccus radiodurans
24. KEY: Activity for Review of
Unit 08.2
Which are true of the eocyte hypothesis?
a. It presents a competing view of the origin of
the domain Eukarya. TRUE
b. It presents a competing view of the structure
of the domain Eukarya. FALSE: the eocyte tree
still has 5 eukaryotic supergroups.
c. It suggests that the closest relatives to the
Eukarya are the eocytes. TRUE.
d. It is a different understanding of the root of
the tree of life and thus LUCA. FALSE: the root
is still in the bacteria, determined by
constructing trees from ancient paralogous
proteins.
25. KEY: Activity for Review of
Unit 08.3
1. What are some reasons why bacteria from the rare phyla
remain uncultivated?
• As with the Chlamydia, uncultured microbes might have undergone
reductive evolution and rely on a host to reproduce
• As with Thermus, high temperatures and oligotrophic (slow)
growth might make cultivation without contamination difficult
• Cryptic micronutrient requirements, Auxotrophy, or require specific
metabolic partners
• As with Planctomycetes and Deinococcus, it may not be clear why
they remain uncultivated.
2. For each pair of phyla below, circle the phylum that is the
most phylogenetically diverse.
• Proteobacteria or Chlorflexi
• Deinococcus or Firmicutes
• Chlorobi or Bacteroidetes
• Candidate Phylum Radiation or Chlamydia
26. KEY: Activity for Review of
Unit 09.1
• How do we get our microbiomes?
– Babies are born with very few microbes, and
acquire their microbiome from their mothers at
birth. Microbes are constantly introduced from the
outside, but our microbiome helps our human cells
to acts as a barrier.
• How does the human microbiome functional
diversity compare to the phylogenetic diversity.
– Despite variation in community structure
(phylogenetic diversity), metabolic pathways tend to
be stable among individuals (functional diversity).
27. KEY: Activity for Review of
Unit 09.2
• Match the eukaryotic superkingdom to its major
characteristics
1. Excavates - b
2. Chromalveolates
- a
3. Plantae - e
4. Rhizaria - c
5. Unikonts - d
a) mostly phototrophic algae,
diatoms
b) flagellated single-celled
eukaryotes, pathogens
c) all unicellular eukaryotes,
very diverse
d) include Amoebozoa and
Opisthokonts, which have two
main groups, fungi animals
e) plants, including land plants,
green and red algae; all have
plastids (chloroplasts) derived
from cyannobacteria
28. KEY: Activity for Review of
Unit 09.3
• Compare the mechanism of action for
probiotics and prebiotics. Which is proven to
be effective in changing the microbiome?
– Probiotics are live microbes that are eaten, and
prebiotics are foods that the host cannot eat,
but feed specific microbes in the gut
microbiome.
– Although some probiotics have shown promise in
research studies, strong scientific evidence to
support specific uses of probiotics for most
health conditions is lacking.
29. KEY: Activity for Review of
Unit 10.1
• Which statements are true about
permafrost?
a) It has an active layer which freezes and
thaws in cycles. - TRUE
b) It is colonized by bacteria, archaea and
eukarya. - TRUE
c) Soils frozen for two or more weeks are
permafrost. – FALSE, two or more YEARS
d) Permafrost can be frozen soils but not frozen
sediments. – FALSE they can be either or a
mix
30. KEY: Activity for Review of
Unit 10.2
1. Name one phylum or class of Archaea.
– Crenarchaeota, Euryarchaeota, Thaumarchaeota,
Koryarchaeota, and Nanoarchaeum
2. For the list of Archaeal traits below, circle
which ones are shared with the Eukarya
a) Information-processing machinery
b) Ether-linked membrane lipids (this trait is unique
to Archaea)
c) Cytoskeleton (this trait is shared with Bacteria, not
Eukarya)
d) Nucleosomes
e) Flagellar structure (this trait is unique to Archaea)
31. KEY: Activity for Review of
Unit 10.3
What are the effects of thawing permafrost?
• Permafrost stores twice as much C as what is in
the earth’s atmosphere right now. The biggest
effect of thawing permafrost is to the carbon
cycle. Thawing permafrost will release
geothermal CH4, a potent greenhouse gas.
Though in the short term, plant growth on
thawed soils will be a sink for C, thawing
permafrost will also increase microbial activity,
releasing CH4 and CO2. Thawing permafrost will
also release mercury and cause the growth of
microbes frozen or dormant for thousands of
years. This includes spore-forming bacteria and
viruses.
32. KEY: Activity for Review of
Unit 11.1
• Match the virus with the hypothesis of origin
of evolution that best describes it.
1. __c__ Mimivirus
2. __b__ HIV
3. __b__ Bacteriophage Mu
4. __a__ Rhinovirus
5. __c__ Klosneuvirus
6. __a__ Rice yellow mottle virus-associated viroid
a. Virus-first hypothesis
b. Progressive hypothesis
c. Regressive hypothesis
33. KEY: Activity for Review of
Unit 11.2
Describe how Koch’s postulates were attempted to be applied to the
discovery of prions as the infectious agent in Mad Cow disease
(Bovine Transmissible spongiform encephalopahty, or TSE). How might
one come closer to satisfying Koch’s postulates?
• Koch’s postulates are the way to prove causation, in this case the
causative agent of infection. To satisfy Koch’s postulates, you’d
have to isolate the infectious agent from an organism with the
disease, re-infect an organism and recreate the disease state,
then re-isolate the same infectious agent.
• In this case, the infectious agent is an alternate conformation of
a folded protein. It is not so easy to measure the folding of a
protein; usually this requires x-ray crystallography.
• This is also complicated by the fact that TSE can arise
spontaneously.
34. KEY: Activity for Review of
Unit 11.3
• What is the difference between a virus and a viroid?
– Viruses are larger
– Viruses can be DNA or RNA, viroids are ssRNA
– Unlike viruses, viroids have no capsid or protein shell
– Viruses infect organisms from three domains, viroids infect
only plants (that we know)
• What is the difference between a viroid and a
satellite?
– Viroids direct the host cell to help with replication, satellites
depend on a helper virus
– Satellites can be DNA or RNA, viroids are ssRNA
– Unlike satellites, viroids have no capsid or protein shell