This content provides a comprehensive introduction to the field of microbiology, covering its fundamental concepts, the nature and importance of microorganisms, the tools used to study them, and their historical development. It emphasizes the ubiquitous presence and diverse roles of microbes in basic life processes, human benefit, and the environment.
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i'm dr d dr d dr d dr
d dr d dr d
dr d explain stuff
hey everyone dr d here and in this video
we are going to be covering chapter one
from our brock biology of microorganisms
15th edition textbook
and this chapter introduces the
microbial world so
let's go ahead and get started
so in this introductory chapter we are
going to be covering
main concepts such as what is microbiology
microbiology
about and why is it important the
structure and activities of microbial cells
cells
evolution and diversity of the cells
microorganisms and their environments
and the impact of microorganisms on humans
humans
so let's get started with the first
theme what is microbiology about and why
is it important
microbiology is the study of mic
the study of microorganisms and how they work
work
microbiology revolves around two
interconnected themes these are the two
main themes of microbiology
understanding basic life processes this
is the basic
science behind uh
behind the microbes so how is the microbe
microbe
growing how is the microbe sending
signals how is the microbe uh deciding
whether or not to
form an endospore how is you know what what
what
makes the microorganism tick how does cellular
cellular
signaling occur in the microorganism
and then the second prong of
microbiology looks at
applying that knowledge that basic science
science
for the benefit of humans this is called applied
applied
science so think about what is the role
of microorganisms in our understanding
of medicine
in our ability to improve agriculture
and our ability to use those
microorganisms for their
utility and industry and all the
products that you can produce
with the help of those microorganisms
and microorganisms are really all around us
us
just look at this figure here figure 1.1
you have image a and in a you can see
a community and remember in biology a
community means
different species of organisms look at
the microbial community
here from a small michigan lake
you have microorganisms galore
everywhere you look in the environment
look at in b a sample of sludge
a sewage sample and look at the
community of different microorganisms
there and you are no exception the human tongue
tongue
there's a host of different
microorganisms living
on your tongue uh in fact there are more
microorganisms that live on your body
than you have total number of cells
of your own did you catch that so there
are more
micro organisms on you
than you have your own cells
now let me explain that in your mouth is
still considered on
you because it is not inside of your tissues
tissues
inside of your mouth if follow that down
to the esophagus
follow that down to the stomach the
intestines and the colon which is the
lower intestine
and you will know that all of that is considered
considered
on you and not in you so what's going on
inside of your colon
is still technically not considered
in your body it's considered on your
body right so your skin
is on top of your body but also the
inside of your mouth is considered
on top of your body and inside of your
stomach inside of your intestines inside
of the
colon etc all of that is
on you not in you when i say inside
of an organism what i mean is inside of
the actual
flesh right inside of your tissues
there should not be any micro organisms
inside of your tissues where the microorganisms
microorganisms
appear is on your tissues and that includes
includes
the lining of your intestines and if you
were to count the microorganisms
on you which again it includes on top of your
your
uh you know your intestines lining the
inner lining of your intestines and
colon and such
you have more microorganisms on your
body right now
then if you were to count your own human
cells you'd be outnumbered isn't that
interesting to think about
now that we know we're surrounded by
these microorganisms why are they so important
important
well they are the oldest form of life
billions of years
before plants and animals we had microorganisms
microorganisms
all those individually small they are
the largest
mass of living material on earth so if
you took
the biomass of microorganisms
that's the largest living mass
on earth they outnumber us like i just
mentioned they outnumber us on our very
own bodies
so they're going to outnumber us in
terms of total
mass as well they carry out major
processes for biogeochemical cycles
they are vital to our appearance as a
species did you know
the earth was anoxic billions of years
ago that means there was no oxygen
in our atmosphere and we can thank these
microorganisms for producing the oxygen
that we breathe and we can thank them to
this very day
for producing the oxygen that we breathe
a lot of people
believe that it's plants and trees that
produce the majority
of the oxygen that we breathe
however it's really thanks to the
microorganisms including the
cyanobacteria which are photosynthetic bacteria
bacteria
and thanks to uh the
diatoms which are photosynthetic
eukaryotes and
obviously other types of algae as well um
um
which are multicellular or unicellular
eukaryotes thanks to these
microorganisms that are photosynthetic
producing oxygen you're able to breathe
right now and of course plants and trees
play a role as well
but they're not the major drivers
for oxygen in our environment and not only
only
producing the oxygen for our environment
but all of these photosynthesizing microbes
microbes
plants trees these photosynthesizers
are also like co2 sponges
through a process known as carbon fixation
fixation
they can take co2 out of the air like a sponge
sponge
removing co2 from the air from the atmosphere
atmosphere
lowering that greenhouse gas in the atmosphere
atmosphere
and making it more habitable for us as a
these organisms can live in places
unsuitable for other organisms you can
find them in
extreme habitats i'm talking extreme hot
extreme cold extreme salt etc extreme
pressure under the ocean
and other life forms require microbes to
survive we'll be touching on this as we
go on but some
organisms require microbes to survive
for their very existence
isn't that neat so what do we use to study
study
these microorganisms well we can use
microscopes obviously
these micro organisms got their name
from being microscopic being too small
to be seen by the naked eye did you know
that your eyeball
can only resolve down to
0.2 millimeters you know what a
millimeter is right
well think about 0.2 millimeters
this is known as 200 micro
meters that's about the resolution limit
of your eyeball
anything smaller than 0.2 micrometers
is just too small to see with your naked eye
eye
does that make sense and these microorganisms
microorganisms
are typically smaller than 0.2 micrometers
micrometers
eukaryotic microorganisms are much bigger
bigger
than prokaryotic microorganisms but they all
all
tend to be smaller than the resolution
limit of your eyeball which is what again
again
it is 0.2 micro uh millimeters which is
200 micrometers
so we need microscopy we need special lenses
lenses
in order to resolve the image and to
magnify the image so that we can see the specimen
specimen
we need to be able to culture the
bacterium so we can grow them in
sufficient numbers to study
and to do so they need medium which is the
the
either liquid or solid mixture
containing the required nutrients that
they need to grow
and then we need to grow them to form a
visible colony so here you can see
a petri dish with a bioluminescent that means
means
light emitting colony of the bacterium
uh photobacterium grown
in laboratory culture on a petri plate
so look at this this is an actual
bioluminescent bacterium not neat
and what this is called is it this is
called a streak
plate you have three zones to a streak plate
plate
and in the third zone you see these dots
these are individual colonies
and an individual colony is called a
clonal population you have
millions and millions you could have
a single colony can contain 10 million
more than 10 million
individual cells in a single colony on a
petri dish
and that's called a clonal population
which means that
they're all clones genetic clones of one another
another
because bacteria divide by asexual reproduction
reproduction
there's no genetic variability that
happens when
after asexual reproduction after binary
fission a cell divides into two cells
those cells are genetically identical
those cells divide again
into four cells which are genetically identical
identical
so pretty soon you have 10 million cells
as in a colony
and all of those cells are genetically
identical they are all clones of one another
another
so when you go into the microbiology lab
and you see little colonies on your
petri dish
just realize that each one of those
little dots
harbors 10 million or more
bacterium and all of them are clones of
one another in that
particular clonal colony and that interesting
interesting
so recall from biology 1406 what
is a cell what is a cell by definition
a cell is a dynamic entity
that forms the fundamental unit of life
remember viruses are not cells nor are
they alive
remember that there are uh unicellular
organisms uh and there are multicellular organisms
organisms
there are prokaryotic organisms and
eukaryotic organisms
unicellular whereas eukaryotes can be
unicellular such as the protists you
know the protozoa
fungi some of the fungi these are
unicellular organisms
and then you can have multicellular
eukaryotic organisms as well
such as you and me right the animals the
plants etc
now let's look at some of the elements
of microbial structure
so microbial structure what do they
tend to have well they have a cytoplasm
they have a cytoplasm and remember the
cytoplasm is an aqueous mixture
of macromolecules ions and ribosomes
and surrounding the cytoplasm you have
the cell
membrane also known as the cytoplasmic
cell membrane
this is the barrier that separates the
inside of the cell from the outside environment
environment
all cells have a
plasma membrane around the cell
eukaryotic cells have a plasma membrane
prokaryotic cells have a plasma membrane
now the composition of that membrane can
vary a little bit
but all cells have a form of plasma
membrane around the cell eukaryotic and
prokaryotic cells
ribosomes microorganisms have ribosomes
remember this is the
the organelle that that synthesizes
proteins uh now keep in mind
although ribosomes are organelles they
are not
membrane bound organelles remember that
prokaryotes do not possess
typically do not possess membrane-bound organelles
organelles
and then you have a cell wall microorganisms
microorganisms
tend to have a cell wall in addition to
the plasma membrane they have an
external cell wall
of some sort that does not mean all
but that means most most microbes
have a cell wall and that confers
structural strength
and it has other functions as well and
it keeps
the cell in a particular shape you'll
learn later in the chapter that cells
can be caucus shape or
rod shape or spiral shape or vibrio or
comma shape
bacteria have different shapes to them
and the reason they can hold that shape
is because of the cell wall now some bacteria
bacteria
don't have a particular shape they're
called pliomorphic
and the reason for that is because those bacteria
bacteria
don't have a cell wall
and keep in mind that animal cells
like your cells and my cells we lack a
cell wall whereas some other eukaryotes like
like
plants and fungi they do possess a cell wall
wall
this should be mostly review
from your bio one class you have the typical
typical
prokaryotic cell here is a cartoon and
on the right you have
the electron micrographs of a bacteria cell
cell
and an archaeal cell and on the bottom
you have the cartoon of
a eukaryotic cell and this and uh
i believe this is a scanning elect no
transmission electron micrograph
of a eukaryotic cell and remember
that eukaryotic cells have
membrane-bound organelles
whereas prokaryotic cells do not have
membrane-bound organelles
and what are the membrane-bound
organelles let me list some off for you
right now
the main membrane-bound organelle people refer
refer
to is the nuclear membrane you know the reason
reason
you have a nucleus is because the
genomic material the chromosomes
are inside of a double membrane called
the nuclear membrane
prokaryotes they don't have a nuclear
membrane they don't have a nucleus
their single circular chromosome
is hanging out in the cytoplasm as
nucleoid did you follow that so
typically all cells have a
gene a genome have a at least one chromosome
chromosome
prokaryotes typically have one chromosome
chromosome
and it's circularized isn't that neat
prokaryotes have a circularized chromosome
chromosome
that means there's no beginning to the
chromosome and there's no end to the
chromosome it's just
a double strand dna circle and
prokaryotes typically have only one
circularized chromosome one chromosome
and that chromosome is not inside of a
double membrane
known as this nuclear membrane you see
so the the dna then is just
called nucleoid it's nucleoid this
if you were to take this dna out unravel it
it
it would look like a giant circle right
if you were to untangle this dna it
would look like one giant circle
whereas with with eukaryotic cells
you have you know let's say humans
humans have 46
pieces of dna 46 chromosomes typically
and those are linear chromosomes which
means if you were to
untech sorry if you were to untangle them
them
they would look like one giant string
with a beginning
and an end isn't that interesting so anyway
anyway
the main membrane-bound organelle
is the nucleus with
you know the nucleus which is lacking in
prokaryotes what are some other membrane
bound organelles of eukaryotic cells
well you have your endoplasmic reticulum
both the smooth and the rough
endoplasmic reticulum
you have the golgi apparatus you have
mitochondria in plant cells
in plant cells you would have the
central vacuole
you would have the chloroplasts
as well these are all membrane bound
organelles and these are lacking
in the prokaryotic cells but remember
what i said in the last slide
you do find non-membrane bound
organelles in prokaryotes such as
ribosomes you know which are found in
both eukaryotes and prokaryotes
and don't forget microorganisms
especially the bacteria typically have a cell
cell
wall in addition to the plasma membrane
they have a cell wall see this is the
cell wall and we'll discuss what the
cell wall is
constructed of later on so again this is
what i was touching on in the previous slide
slide
where you're comparing prokaryotes
versus eukaryotes
remember that prokaryotes are generally
smaller than eukaryotic cells by quite a
quite a bit a typical prokaryotic cell
is about
10 to 50 times smaller than a eukaryotic cell
cell
eukaryotic cells are larger and they
contain all these membrane-bound organelles
organelles
including the main one remember which is
the nucleus
but that doesn't mean that prokaryotes
don't have dna
remember that prokaryotes typically do
have a chromosome and it's a
circularized piece of double strand dna
which makes up their chromosome which
makes up their
their genome okay so again no membrane bound
bound
organelles no nucleus instead they
possess a nucleoid
okay whereas the eukaryotes they do have
a membrane-bound
nucleus and they're generally more complex
complex
and larger and they contain all of these membrane-bound
membrane-bound
organelles and remember we talked about
the genome
very important that you have a genome
and and the genome is the cell's
full complement of genes and those
genes reside on chromosomes right
again prokaryotes have a single
circularized chromosome that aggregates
uh to form the nucleoid whereas
eukaryotes have linear chromosomes you
know with humans having 46
within the nucleus we also have
much more dna eukaryotes have a lot more
nucleotides a lot more dna like humans
have over 3 billion
base pairs prokaryotes it's usually a
few million
base pairs now so their genomes are
quite a bit smaller
prokaryotes may also have extra
chromosomal dna called plasmids these
are small
circularized dna that can replicate
independently of the main chromosome
okay and these can have special genes on
them that confer
special properties like there might be a
gene on a plasmid for
antibiotic resistance or there might be
a gene on a plasmid that
that codes for a toxin right so look at this
this
this is your main chromosome which is
the large circularized piece of dna
inside of a cell and then you have your
tiny little guy this is a plasmid it's a small
small
piece of circularized dna that
replicates independently of the chromosome
chromosome
and again it can harbor genes important genes
genes
such as antibiotic resistance or toxins
okay and don't forget the the genome
the genome of a prokaryote is in the
millions of base pairs usually i believe
with uh e coli for instance it has about
4.6 million base pairs if i'm
remembering correctly
okay and remember that like i showed you
earlier from the human tongue
sample and the sewage sample and the
lake sample
in nature cells typically live in microbial
microbial
communities and remember in biology
community means
different species inside of a
you know in an area they also undergo
metabolism right cells undergo
metabolism and microbes are no
exception this is chemical
transformation of nutrients
you know you need to take up sugars you
take up
fats and then you could digest those
sugars and fats in order to produce atp
in order to promote you know the
functions of the cell
don't forget you also have enzymes to
assist during metabolism
you have other processes as well like transcription
transcription
and translation going on in the
microorganisms this is how they're
undergoing gene expression
so don't forget these are properties
of all cells do you remember from
biology 1406 that all
cells undergo metabolism which again
includes catabolism and anabolism
catabolism is breaking down substances
anabolism is building substances
you you know genetic replication
transcription translation would be anabolism
anabolism
breaking down sugars and fats for energy
that would be
catabolism this is all part
all of the chemical processes inside of
the cell
are together known as metabolism
all cells all cells grow
uh and they can grow from you know
digesting the nutrients inside of
solutions inside the media that they're growing
growing
now obviously grow means a different
thing to a prokaryote than it does to a
multi-cellular eukaryote like you and me
when you and me are discussing growing
that means growing
up or growing in size growing from a
child to an adult
you know this is organ or organ
development this is tissue development
this is
your bones lengthening etc maturation
but in prokaryotes remember prokaryotes
are typically single cell creatures
so grow means a slightly different thing
grow could mean
you know the cell grows slightly in size
right the cell to mature right one cell
to mature
okay and all cells evolve evolution means
means
changes in gene frequencies over time or
changes in genetic material over time
all cells evolve now what are some
properties of some cells
some cells have the ability to differentiate
differentiate
we're going to learn about how some some
bacterium including
bacillus and clostridium genuses
have the ability to differentiate from a
vegetative cell into a spore
an endospore to to protect their
themselves to protect their genomic uh
you know
complement we can talk about how
some cells can communicate with other
cells you know this is called quorum sensing
sensing
where cells can actually communicate
with one another and
and uh you know and it's in the benefit
of the
of the community they can
genetically exchange information they can
can
they can share genetic information with
one another
even across species you know some cells
have the ability to
undergo what's known as horizontal gene
transfer which means
sharing genetic information from one
cell to another is fascinating stuff
we're going to talk about
some cells are modal they have a flagella
flagella
or some other form of motility that
allows them to propel
through through media okay we touched on this
this
material now a little bit about the history
history
of life on earth and the importance of microorganisms
microorganisms
during that stretch during that history
the earth is 4.6 billion years old
and the first cells these would have
been prokaryotic cells appeared about
3.8 to 4.3 billion years ago
and at the time remember i had mentioned
that the atmosphere was anoxic
so no oxygen in the environment
but it was due to these anaerobic
uh bacterium that
over time life expanded
in the absence of oxygen and the first
anoxic or an oxygenic phototrophs
these are photosynthetic bacterium
uh came about 3.6 billion years ago
and thanks to them one of their waste
products was oxygen so as
these bacterium these phototrophs grew
one of their byproducts their waste by-products
by-products
was oxygen and so oxygen started to
accumulate in the atmosphere
and over time there was more and more
oxygen to the level there is today uh
you know now we have about 20 percent
oxygen in the atmosphere
and it's thanks to these phototrophs is
thanks to these photosynthesizers over time
time
and that's what allowed organisms like
you and me to
to come about these plants animals
to come about about a half a billion
years ago
we were we had the ability to come about
because there was now oxygen in the atmosphere
atmosphere
and we still require these
microorganisms and require these photosynthesizers
photosynthesizers
producing the oxygen in the atmosphere
that we need to breathe
to to persist and here you can see
that again what what we're discussing that
that
the earth is about 4.6 billion years old
the life began somewhere around
you know just shy of 4 billion years ago cellulite
cellulite
presented itself the earth was
an oxygenic so no oxygen
but those photosynthesizers of cyanobacteria
cyanobacteria
were able to photosynthesize producing
oxygen waste products and that allowed
modern eukaryotes to come about
algal diversity over time and then finally
finally
again half a billion years ago plants
and animals
and ultimately humans to uh present themselves
themselves
so isn't that interesting to think about that
that
you and i breathe the waste products of
other organisms these organisms
grew over time producing the waste product
product
oxygen and now we rely
it is vital for our
survival that we have access to this
waste product from other organisms that
blows my mind every time when i think
about it
and to this day we require these algae
these cyanobacteria these plants these diatoms
diatoms
these trees constantly sucking up
co2 like a sponge out of the atmosphere
to lower climate change and produce
oxygen required for us to breathe
so that we can live on in that interesting
interesting
recall from biology 1406 that there are
three main domains of life
three distinct lineages of microbial
cells we have
bacteria which are comprised of
prokaryotic cells
archaea prokaryotic and then eukarya
these are the eukaryotic cell organisms
and we all are thought to have descended
from the last universal
common ancestor known as luca for short
you see here
we had a last common ancestor some
billions of years ago
and then from there branched off to the
domains of life archaea i'm sorry archaea
archaea
bacteria and eukarya notice too
hopefully they touched on this in
biology 1406 but if not
realize that eukarya and archaea
are more commonly related more
related than either is to bacteria
that's another of one of those
mind-blowing things to understand that
that archaea and bacteria even though
they look the same under the microscope
and even though they're both comprised
of prokaryotic cells
they are very different genetically archaea
archaea
are much more like us genetically than
they are
to bacteria that's why archaea and
bacteria are no not
in the same domain of life even though
they share so many
common uh phenotypic characteristics
okay so it is thought that archaea and
eukarya share a more
common ancestor than either does
to bacteria which is the last the
common ancestor the last universal
common ancestor
it is thought that there's about two times
times
two times ten to the 30 microbial cells
on earth that's a lot of biomass
and keep in mind these creatures can live
live
anywhere on earth including extreme environments
environments
of too harsh for other organisms to live
like hot springs
glaciers high salt conditions high
acidity high alkalinity
high pressure etc remember your
this is where your your archaea will live
live
and remember that ecosystems refer to all
all
living organisms plus their physical
and chemical environment so if i'm
talking about an ecosystem
that includes the community plus the environment
environment
so not just the fish and the um
tadpole and the and the frogs and the and
and
and the sharks but the the actual ocean
as well for instance
uh metabolic activities can change
habitats and affect
other organisms obviously the whole
reason we have oxygen in our environment
is the byproduct of this metabolic
activity so
so what the organisms are doing in in a
in an environment can affect the actual habitat
habitat
and affect other organisms and
the field of microbial ecology is the
study of microbes in their natural habitat
habitat
and how that affects other communities
as well or other populations as well i
should say
in humans 1 to 10 microbial cells per
human cell this is what i was touching
on earlier
for you in humans you have
more bacterial cells on your body right now
now
then you have your own number of cells
think about that
it's very interesting stuff and this
table just
shows you just a taste of where
these extremophiles live these these uh
organisms that could live in extreme
conditions remember high temperature
low temperature low ph high ph high
pressure high salt
wherever you look every nook and cranny
on earth has some kind of life
on it and that's how you can get such a
huge biomass
of microbial organisms so microorganisms
can be both beneficial
and harmful to humans obviously
we're dealing with a pandemic right now
and that's due to a virus
not necessarily a living
organism however many
microorganisms including bacteria
fungi protozoa you know these little protists
protists
fungi they can all cause human diseases
so microorganisms can affect
our health but they can also be
beneficial just look at their uses
in food the production of
fermented foods in agriculture
sometimes they're vital for certain agricultural
agricultural
products and also in in
industry as well we utilize these microorganisms
microorganisms
in all aspects of different forms of
and like i mentioned microorganisms as disease
disease
agents it's a big deal uh with the
advent though
of vaccines and antibiotics
we have been able to for the most part
control these infections
however they continue to become you know
more and more of a problem as more and
more microorganisms
become resistant to antibiotics and they adapt
adapt
and there's evolution going on so we
have to constantly
evolve our ways of combating disease
however don't forget that most
microorganisms are beneficial i mean
like i said you have more microorganisms
living on your body right now
then you have your own number of cells
and many of those are
what are known as beneficial or probiotics
take a look here what i was touching on earlier
earlier
this is a this is a chart from uh of
data from
1900 the year 1900 and here's a chart of
data from closer to today
and in red you can see in the red bars represent
represent
these are microbial diseases and the
effects they've had on human death
notice that in in the year 1900
the biggest killer of human beings was
the flu
and pneumonia followed by tuberculosis
which is also a microbial disease
gantry gastroenteritis also a
microbial disease and it's not until the fourth
fourth
tick down that you see that human that
heart disease
heart disease which is not a microbial uh
uh
disease was you know the fourth leading killer
killer
of humans fast forward to today
uh you have to go quite a bit down the
chart before you find
uh a microbial uh you know a microbial
cause of human disease
and human death why because like i mentioned
mentioned
the advent of antibiotics
vaccinations improved sanitary
conditions and our understanding of germ theory
theory
and how diseases spread isn't that
fascinating that now
we have learned so much because of the
field of microbiology
that now we can turn our attention to
other causes of human suffering and
human death
and to focus on those and hopefully one
day rid those
as well another important aspect
of the impact of microorganisms is their impact
impact
in agriculture where they have both
positive and
negative implications so you can see
the positive impacts of microorganisms
is their ability to fix
nitrogen just like they can fix co2
which means to remove
co2 from the air they can also fix
nitrogen they can actually remove
nitrogen from the air
and from that nitrogen they can produce ammonia
ammonia
ammonia is needed by plants and plants
can actually convert that ammonia to
nitrites or nitrates you know things
that they need
to grow they can also
degrade cellulose which humans cannot do
and also animals cannot do and these
cellulose degrading microbes
exist in the rumen of rheumatoids these
are animals like
digest plant matter in order to grow
they can regenerate nutrients for soil
and water
they can also cycle
sulfur by oxidizing toxic
hydrogen sulfide into sulfates
and sulfates are non-toxic and needed
by plants it's an essential nutrient
some of the negative impact
impacts of these plants of these uh microbes
microbes
are is their ability to cause diseases
in plants
diseases in animals so you know
with the good comes the bad but there's
a lot of good
that comes from microorganisms
you know in in agriculture here you can
see what i was talking about you have
nodules root nodules on soybean plant
these these harbor bacteria
that can fix nitrogen fix gaseous nitrogen
nitrogen
into ammonia and then the soybean plant
utilizes that ammonia to grow
you can see the the nitrogen cycle by
through nitrogen fixation you can form ammonia
ammonia
and then sulfate or sorry nitrate with the
the
sulfur cycle you can take sulfur you can
reduce that to sulfate
and what what do plants do plants take
the hydrogen sulfide
they then oxidize that
yes oxidize that to sulfur and then the
plants can use the sulfate
products from that reaction the site the
sulfur reaction
in order to grow so sulfate is important
for plants to grow
nitrates are important for plants to
grow and it's thanks to microbial action
that we have
the access to these sulfates and nitrates
nitrates
and you you you can see here the it's
the rumen remember that
uh these removables these these animals
that can digest plant matter you know
they have these multi-chamber stomachs
and in the rumen of these animals you
have microorganisms
that are able to break down cellulose
which is
you know something that animals cannot
normally break down for instance you and
i cannot break down
cellulose into glucose however with the
help of these microorganisms
these ruminant animals are able to break
down cellulose into glucose
and then utilize that glucose in order
to make
you know uh to to utilize that glucose
for energy in the in the
in the animal another impact of microorganism
microorganism
organisms is their existence in our
gastrointestinal tract of humans
remember i told you that there are many microorganisms
microorganisms
in your stomach in your intestines your
small and large intestines colon etc
and this in here they have a lot of positive
positive
impacts for instance the microorganisms
in your digestive system can synthesize
vitamins and other nutrients that you
might need
and where they really come in handy is
their ability
to just take up space you have
good helpful bacteria called probiotics
in your intestinal system
and these probiotics these these helpful bacteria
bacteria
they stick to the lining of your
intestines and they take up space
and that's their utility because there
are some bad
players out there there's an example of
a black
of a bad player called clostridium difficile
difficile
which is a bacteria that if if this
bacteria takes over your guts
takes over your intestines it actually secretes
secretes
a toxin which can really irritate the colon
colon
causing colitis bleeding causing bloody stool
stool
and a lot of human suffering comes from
these c
diff infections right it's but
but when there's a healthy probiotic
layer in your intestine well then those
healthy bacterium
do not allow these clostridium difficile
bacterium to attach they can't take over
so you see the fact that they compete
with pathogens for space and resources
here you can see the stomach the small intestine
intestine
and the large intestine the colon essentially
essentially
and the types of co communities
of microorganisms that live inside there are
are
many different microorganisms that live
in your gi tract you can see here that
in the stomach which is
very acidic with a ph of two or sometimes
sometimes
less you have about 10 to the four
cells per gram in the small intestine
where the ph is more
towards you know less acidic i should say
say
more neutral you can have up to 10 to the
the
eight cells per gram of
microorganisms and in the large
intestine which has neutral ph
you have 10 to the 11 cells per gram you have
have
many microorganisms in your gi tract
and again a lot of these are helpful
they are producing vitamins and other
nutrients for you
and one problem with uh
you know common day antibiotic overuse
you know the over
prescription of antibiotics the overuse
of antibiotics
is that they will go and kill these
helpful probiotics in your intestines right
right
so now all these this community that's
helping you that's taking up space
that's out competing pathogens
these microorganisms die and shed off of
the lining of your intestines
thereby allowing pathogenic bacteria
such as clostridium difficile that i mentioned
mentioned
to attach and grow and populate the
linings of your intestines now this is bad
bad
because that bacterium harms the
intestinal lining
okay very interesting stuff to think about
about
microorganisms also have positive and negative
negative
impacts on our food industry and food supply
supply
the negative impacts include food
spoilage obviously
food gets putrid or goes bad
due to microorganisms there are food
borne diseases
you can get ill from eating microorganism
microorganism
contaminated foods and microbes
influence how we
harvest our food how we store our food food
food
safety how we prevent spoilage of our food
food
all all are with microorganisms in mind
some of the positive impacts though is
that we've improved food safety
how we preserve the food we can produce
so many
neat dairy products with the help of microorganisms
microorganisms
cheeses yogurts buttermilk these are
dairy products that would not be
possible without the help of
microorganisms and people know and love
these items
with these probiotics and then obviously
other food products that
are fermented by microorganisms and
would not exist
without the help of microorganisms
sauerkraut kimchi
pickles chocolate coffee laven breads
beer etc and here we can see
how some of the fermented products lead to
to
our our favorite meals microorganisms
are able to ferment
glucose into different fermentation products
products
some microorganisms form propionic acid
acidic acid co2 as fermentation products
this leads to production of cheese other
fermenters produce lactic acid which
allows us to have
uh types of yogurt and types of
other dairy products we have ethanol
production you know
microorganisms can produce ethanol
through fermentation that leads to wine
and beer and such
acidic acid production which can be used
to pickle
uh cucumbers to make pickles to make
from the fermented foods that we love
not only in not only does the
fermentation process
help produce the food the characteristic
flavor of the food but it also helps to
preserve the food as well these are
these these foods have a natural
preservation to them
to some extent microorganisms can impact
our industries when we
form pipes storage tanks and with
certain medical devices we have to
understand how
biofilms which we'll explain in a later chapter
chapter
how biofilms from microorganisms might grow
grow
and might affect these devices in
industrial microbiology we grow massive
amounts of microbes
that are designed to produce antibiotics
enzymes and some chemicals for us in biotechnology
biotechnology
we genetically engineer microbes to produce
produce
high value products in small amounts
such as
insulin for instance
and we can use microorganisms in the
production of biofuels
you know methane ethanol these are
biofuels that we can use
in our machines and we can use them
in bioremediation to clean up oil spills
solvents pesticides etc here you can see
ethanol being used as a biofuel
and the ethanol is produced by
these microorganisms that are capable of fermenting
fermenting
cellulose from in this example switch glass
glass
switch grass i should say and cornstarch
from corn the the cellulose and the cornstarch
cornstarch
are basically polymers of glucose
microorganisms then ferment
that glucose
into ethanol so you have
breakdown of cellulose and cornstarch
into glucose
fermentation into ethanol and then the
ethanol is stored in these big tanks
and used as biofuels used in
flex fuel cars for instance now before
we move on to
part two of this chapter microscopy in
the origins of microscopy
since this is a new uh new area
of this of this chapter let's go ahead
and take a quick little
break give ourselves a chance to unwind
grab a drink or something
so let's take a quick break time with
gizmo and wicket and we'll be right back
[Music]
all right welcome back from break time
with gizmo and wicket let's continue
chapter one with our discussion of microscopy
microscopy
so in this part of the chapter one we're
going to talk about
light microscopy improved
contrast microscopy
imaging cells in three dimensions and
also electron
microscopy so microbiology the field
began with the advent of the microscope
we can thank a couple of pioneers for this
this
robert hook and anthony van leeuwenhoek
robert hook using some early
lenses in order to describe microbes
and publishing some of those early early images
images
some of the first images of microorganisms
microorganisms
in microgravia in 1665
anthony van leeuwenhoek with his pinhole microscope
microscope
he was the first to describe bacteria
so you can see robert hook
with his early microscope here's a
drawing of his early microscope design
and some of the
some of the small microbes he was able
to see these are some
uh fun fungi that he saw growing from a
piece of leather
that he had anthony van leeuwenhoek had
you know he was a haber dasher by day
haberdasher is a men's
outfitter of the time so he would uh
you know provide gentlemen with
suits and hats top hats and canes and
such but as a
hobby he would on the side you know
work with optics work with lenses and he
created this
pinhole microscope which is a tiny hole
that's the pinhole right there
with the lens in it that lens was able
to magnify
almost 300 times and
the specimen would go on the tip of this pin
pin
and so he would look through this hole
at the specimen at the tip of this this needle
needle
and he would he would look at and see
shapes that we currently know as
microbes he would find caucus-shaped
microorganisms he would see rod shape
spiral shape organisms as well
here you can see some blood cells that
he he was able to resolve
as well so with the advent of these
this these optics these lenses that
could magnify
the microbial world we gained an
understanding of these microorganisms
microbiology
so this is now called a light microscope
when you're using
visible light in order to magnify an image
image
and remember visible light is you know
it encompasses the the wavelengths from
about 300
nanometer emissions to 700
nanometer emissions so from purple all
the way to red
visible light and with these
lenses you're able to magnify an image
and gain resolution so what's the
difference between
magnification and resolution
magnification is
how many times larger is the
object than the specimen really is
if the object appears twice as big as
the specimen really is then you have a
two times magnification if it appears ten
ten
times larger you have a 10 times magnification
magnification
now resolution on the other hand is how
how sharp that image is
it's the ability to distinguish two
adjacent options
objects as distinct and separate so
think about it this way if i have two
tiny dots
and they're getting closer and closer
and closer at what point do those two
tiny dots that are not touching
at what point do they appear as one dot that
that
is the definition of resolution
so the closer those two dots can get and
still be distinguished as two separate dots
dots
that is uh your that is that is your resolution
resolution
okay and without resolution
everything will appear blurry and
remember what i told you
the resolution limit of your eye was
0.2 millimeters well
the resolution limit for a light
microscope is about
0.2 micrometers so
it's a thousand times better than your eyeball
eyeball
so we're able to magnify and resolve
a thousand times better
than with a naked eye right
and that's why our microscopes have a
maximum setting of
1000x when you engage the oil objective
now the compound light microscope uses a series
series
of lenses and there are two magnifying lenses
lenses
remember the compound light microscope
is the same as the one you're using in lab
lab
it has a rotating nose piece with
objective lenses that change
remember there's a 10x a 40x
and 100x lens on there that's the oil
immersion lens
but you also have an ocular lens an eyepiece
eyepiece
and the ocular lens magnifies as well
that magnify is usually 10x right so
your microscope effectively magnifies
between 100x and 1000x
that's your range that you're working
with and there are many different types
of light microscopy
there's bright field phase contrast
dark field and fluorescence now the ones
that you're using in lab
are actually capable of these first three
three
and the and the way you switch between
these first three is by rotating
the condenser remember the condenser
either says
a or o that is bright field microscopy
you slide that condenser over and if it
says ph1 ph2 or ph3
that's phase contrast microscopy and if
you slide that condenser again
you'll see df for dark field microscopy
so we're going to touch on each of these
let's start with compound light
microscopes a compound light microscope
uses visible light to eliminate
illuminate cells but not only that
it has two sets of lenses to form an image
image
remember you have the objective lenses
these are your the ones that are on that
rotating nose piece
and then you have your ocular lens which
is your eye
piece which magnifies as well so the
total magnification
is the product of objective
magnification and ocular
magnification all right so again if if
you're on the 40x objective
you have to multiply that by the
magnification of the ocular which is 10x
so you're adding a total magnification
of 400x
and a bright field microscope with the
bright field microscope special
specimens visualize because of
differences in contrast
between specimen and surroundings
now contrast is a term i need you to know
know
contrast is how much
the specimen stands out against the
background okay that's what contrast
means this is the reason we stain ourselves
ourselves
sometimes you need to stain your cells
that's so that
the cell will become purple or pink or
green or colored in some way that it
stands out
better against the background that's why
we stain ourselves
and here you can see a compound like
microscope such as the ones we have in
the lab
you can see it has the different parts
that you should be aware of the ocular lens
lens
you have the objective lenses on this
rotating nose piece
you have the stage the condenser is the lens
lens
underneath the stage and remember the
job of the condenser is to
focus a cone of light onto the specimen
then you have the iris the iris is
usually right here
the iris is a diaphragm that restricts
the light and when you restrict the
light with the diaphragm
you increase contrast you have the coarse adjustment knob
coarse adjustment knob you have the fine adjustment knob and
you have the fine adjustment knob and the light source
the light source okay so this is a compound light
okay so this is a compound light microscope and on the right with figure
microscope and on the right with figure b
b you can see how the light works you have
you can see how the light works you have the light source
the light source travels through the condenser lens with
travels through the condenser lens with the condenser focuses a cone of light
the condenser focuses a cone of light onto the specimen
onto the specimen the light then travels through the
the light then travels through the objective lens
objective lens through the ocular lens and then it's
through the ocular lens and then it's visualized by your eye
and this is the types of images you can see
see with a bright field microscope you can
with a bright field microscope you can see this is purple
see this is purple phototropic bacteria and this is green
phototropic bacteria and this is green algae now these are cells that have not
algae now these are cells that have not been stained
been stained but have a natural stain to them they
but have a natural stain to them they have natural pigmentation
have natural pigmentation that's why they have a natural type of
that's why they have a natural type of staining to them
staining to them however if you're trying to resolve uh
however if you're trying to resolve uh specimens that don't have a natural
specimens that don't have a natural pigment like
pigment like chloroplasts for instance well then you
chloroplasts for instance well then you might want to
might want to consider staining your specimen so it
consider staining your specimen so it actually has some contrast to it
actually has some contrast to it okay so again staining improves contrast
okay so again staining improves contrast dyes are organic compounds that bind to
dyes are organic compounds that bind to specific
specific cellular materials now
cellular materials now most of the dye that we use in lab
most of the dye that we use in lab remember we use
remember we use dyes such as crystal violet methylene
dyes such as crystal violet methylene blue
blue malachite green we use different types
malachite green we use different types of dye
of dye don't we in the lab most of them are
don't we in the lab most of them are basic
basic dyes basic dyes have a positive
dyes basic dyes have a positive charge to them and they work great for
charge to them and they work great for staining
staining the overall cell because most cells
the overall cell because most cells are strongly negative charged at the
are strongly negative charged at the surface
surface most cells have a negative charge at the
most cells have a negative charge at the surface
surface so why not use a basic dye a positively
so why not use a basic dye a positively charged dye
charged dye that sticks well to that charge okay
that sticks well to that charge okay again methylene blue crystal violet
again methylene blue crystal violet safranin these are all examples of basic
safranin these are all examples of basic dyes
dyes and basic dyes are great for staining
and basic dyes are great for staining cells so you can determine general
cells so you can determine general shape of the cell general morphology of
shape of the cell general morphology of the cell
the cell arrangement of the cell etc
arrangement of the cell etc okay and don't forget we learned this in
okay and don't forget we learned this in lab
lab how to prepare a smear you would take
how to prepare a smear you would take bacteria and spread it
bacteria and spread it in a you know a circle circular pattern
in a you know a circle circular pattern the size of a nickel or so on a slide
the size of a nickel or so on a slide allow it to air dry heat fix
allow it to air dry heat fix then flood the slide with stain
then flood the slide with stain then after the stain you gotta rinse it
then after the stain you gotta rinse it you got to blot it dry with bibulus
you got to blot it dry with bibulus paper
paper check it out under the microscope and
check it out under the microscope and then ultimately go all the way up to oil
then ultimately go all the way up to oil the oil lens with the immersion oil in
the oil lens with the immersion oil in order to resolve
order to resolve those bacterial cells
all right and what are differential states differential stains
states differential stains have you could see different kinds of
have you could see different kinds of cells in different colors
cells in different colors so the most famous of these would be the
so the most famous of these would be the gram stain
gram stain remember that bacteria have two
remember that bacteria have two different uh cell wall architecture in
different uh cell wall architecture in fact we haven't touched on it yet but
fact we haven't touched on it yet but in the next chapter i'm going to explain
in the next chapter i'm going to explain to you how there are two
to you how there are two different architecture of cell wall for
different architecture of cell wall for bacteria
bacteria bacteria are either considered to have
bacteria are either considered to have gram-negative
gram-negative cell wall architecture or gram-positive
cell wall architecture or gram-positive cell wall
cell wall architecture this is the way that their
architecture this is the way that their cell wall is constructed right
cell wall is constructed right and the gram stain distinguishes between
and the gram stain distinguishes between these two architectures so
these two architectures so for example e coli has a gram negative
for example e coli has a gram negative cell wall architecture
cell wall architecture so it will stain pink with the gram
so it will stain pink with the gram stain
stain whereas staphylococcus aureus has a
whereas staphylococcus aureus has a positive cell wall architecture
positive cell wall architecture so when you do the gram stain it will
so when you do the gram stain it will stain purple
stain purple so a gram stain looks for differences
so a gram stain looks for differences in the cell wall structure gram positive
in the cell wall structure gram positive cells and ground
cells and ground negative cells how is the gram stain
negative cells how is the gram stain conducted
conducted first you make a smear of your cell
first you make a smear of your cell then you flood the cell you flood the
then you flood the cell you flood the smear i should say with
smear i should say with crystal violet for one minute this
crystal violet for one minute this stains
stains all cells purple this stains all cells
all cells purple this stains all cells purple because crystal violet
purple because crystal violet is purple next you have to add iodine
is purple next you have to add iodine why do you add iodine iodine doesn't
why do you add iodine iodine doesn't stain the cell
stain the cell iodine acts as a mordant what that means
iodine acts as a mordant what that means is it keeps
is it keeps this dye in place the iodine will
this dye in place the iodine will will join up with the crystal violet
will join up with the crystal violet forming a dye iodine complex
forming a dye iodine complex making the crystal violet less permeable
making the crystal violet less permeable which means harder to wash
which means harder to wash out of the cell next you're going to
out of the cell next you're going to decolorize the cells
decolorize the cells with alcohol so you add you briefly add
with alcohol so you add you briefly add alcohol drop wise and that washes
alcohol drop wise and that washes the crystal violet out of the cells
the crystal violet out of the cells you see in fact if you were to do this
you see in fact if you were to do this long enough all of your cells would
long enough all of your cells would become clear
become clear all of them would get washed and the
all of them would get washed and the crystal violet would would get out of
crystal violet would would get out of the cells
the cells however if you do this briefly only the
however if you do this briefly only the gram-negative
gram-negative cells because of their cell wall
cells because of their cell wall architecture only gram-negative cells
architecture only gram-negative cells will lose the stain
will lose the stain gram-positive cells especially with the
gram-positive cells especially with the help of iodine holding this
help of iodine holding this the dye in place gram-positive cells
the dye in place gram-positive cells will not lose the coloration
will not lose the coloration gram negative cells will lose the
gram negative cells will lose the coloration will lose the crystal violet
coloration will lose the crystal violet so what happens at this stage is that
so what happens at this stage is that gram-positive cells are purple
gram-positive cells are purple but gram-negative cells should appear
but gram-negative cells should appear colorless and here comes the counter
colorless and here comes the counter stain the second color
stain the second color in the differential stain we're we're
in the differential stain we're we're staining with safranin like a pink red
staining with safranin like a pink red dye
dye and now those clear cells become colored
and now those clear cells become colored pink and even if the pink color gets
pink and even if the pink color gets into the purple
into the purple gram-positive cells this that you know
gram-positive cells this that you know the purple is darker so they still
the purple is darker so they still appear purple
appear purple and what do you see under the microscope
and what do you see under the microscope you see
you see purple cells are your gram-positive
purple cells are your gram-positive cells and the pink cells are your
cells and the pink cells are your gram-negative cells
gram-negative cells so it's a differential stain
so it's a differential stain differential stains allow us to
differential stains allow us to differentiate
differentiate between different types of cells
between different types of cells now we now that we understand how bright
now we now that we understand how bright field microscopy works what about
field microscopy works what about phase contrast microscopy remember that
phase contrast microscopy remember that our microscopes in the lab
our microscopes in the lab are capable of phase contrast as long as
are capable of phase contrast as long as you slide the condenser to the ph
you slide the condenser to the ph setting now when you do that it improves
setting now when you do that it improves the image contrast
the image contrast and it improves it in unstained live
and it improves it in unstained live cells the reason for this is simple
cells the reason for this is simple light that strikes
light that strikes uh the specimen will get slowed it goes
uh the specimen will get slowed it goes through a phase
through a phase plate and that puts the light out of
plate and that puts the light out of phase
phase so it effectively what it does is it
so it effectively what it does is it deletes that
deletes that wavelength of light making the specimen
wavelength of light making the specimen darker
darker than it really is it's like an
than it really is it's like an artificial way of
artificial way of staining the cell so that the cell
staining the cell so that the cell appears darker against the light
appears darker against the light background here you can see
background here you can see some yeast cells
some yeast cells under just regular bright field
under just regular bright field microscopy these are unstained
microscopy these are unstained yeast cells and notice here with the
yeast cells and notice here with the help of phase
help of phase contrast microscopy and no real staining
contrast microscopy and no real staining those cells appear much darker against
those cells appear much darker against the background
the background and that brings out some of that natural
and that brings out some of that natural contrast
contrast same thing with dark field remember we
same thing with dark field remember we could slide our condenser over to the
could slide our condenser over to the dark field setting with the df
dark field setting with the df abbreviation on our condenser and that's
abbreviation on our condenser and that's another way of artificially
another way of artificially improving contrast but a totally
improving contrast but a totally different
different way it allows only
way it allows only light that reaches the specimen to get
light that reaches the specimen to get collected into the objective any light
collected into the objective any light that does not strike the specimen
that does not strike the specimen escapes the objective so what you
escapes the objective so what you effectively get
effectively get is a bright image on a dark background
is a bright image on a dark background so look here this would be a dark field
so look here this would be a dark field image
image where all of the light that did not
where all of the light that did not strike our yeast cells that light
strike our yeast cells that light escapes the objective
escapes the objective and is not collected so it appears like
and is not collected so it appears like a black background
a black background only the light that struck our specimen
only the light that struck our specimen was refracted into the objective and
was refracted into the objective and collected by the objective
collected by the objective therefore your your yeast cells appear
therefore your your yeast cells appear bright against a dark background and it
bright against a dark background and it gives you
gives you excellent uh contrast
excellent uh contrast in living cells especially if you're
in living cells especially if you're trying to observe
trying to observe motility of those cells you can see them
motility of those cells you can see them swimming around and
swimming around and obviously you can't stain a cell that
obviously you can't stain a cell that you want to
you want to study motility because that would
study motility because that would require
require killing the cell so you could look at
killing the cell so you could look at live
live unstained cells that's pretty neat
unstained cells that's pretty neat now what about fluorescence microscopy
now what about fluorescence microscopy fluorescence microscopy
fluorescence microscopy is another form of light microscopy but
is another form of light microscopy but not one that
not one that is readily available to us it allows you
is readily available to us it allows you to
to visualize specimens that fluoresce
visualize specimens that fluoresce this means that they have some sort of
this means that they have some sort of fluorescence property or they are
fluorescence property or they are tagged with a fluorophore a molecule
tagged with a fluorophore a molecule that fluoresces
that fluoresces but either way you have to allow for
but either way you have to allow for fluorescence
fluorescence so and fluorophores or fluorescing
so and fluorophores or fluorescing molecules what they do
molecules what they do is they absorb wavelengths of one uh
is they absorb wavelengths of one uh or light from one wavelength and then
or light from one wavelength and then they emit light
they emit light of a different wavelength does that make
of a different wavelength does that make sense so a fluorescent molecule might
sense so a fluorescent molecule might absorb blue light and then emit green
absorb blue light and then emit green light
light uh and that's what fluorescent molecules
uh and that's what fluorescent molecules do
do okay and one one thing uh one fun fact
okay and one one thing uh one fun fact for you
for you fluorophores or fluorescent molecules
fluorophores or fluorescent molecules always absorb
always absorb light that's shorter in wavelength which
light that's shorter in wavelength which means higher energy light
means higher energy light than the wavelength that they emit they
than the wavelength that they emit they always emit
always emit a longer wavelength or lower energy
a longer wavelength or lower energy light
light so because of this cells appear to glow
so because of this cells appear to glow on black background
on black background because of filters so here you can see
because of filters so here you can see some examples of fluorescence in action
some examples of fluorescence in action you can see
you can see cyanobacteria and these are
cyanobacteria and these are cyanobacteria
cyanobacteria observed with phase contrast
observed with phase contrast microscopy which is a and c and by
microscopy which is a and c and by fluorescence microscopy and b and d so
fluorescence microscopy and b and d so here's
here's here's the cyanobacteria with phase
here's the cyanobacteria with phase contrast here
contrast here in a anc and the same cyanobacteria
in a anc and the same cyanobacteria with fluorescence microscopy here in
with fluorescence microscopy here in b and d you see how the
b and d you see how the cyanobacteria are fluorescing
cyanobacteria are fluorescing they appear to be glowing against a dark
they appear to be glowing against a dark background
background also here in e you can see fluorescence
also here in e you can see fluorescence of cells of e coli sorry this should be
of cells of e coli sorry this should be italicized as
italicized as estericia coli should be italicized uh
estericia coli should be italicized uh these e coli are glowing
these e coli are glowing because of dapi dapi is a fluorescent
because of dapi dapi is a fluorescent molecule
molecule that tightly binds to dna so what you're
that tightly binds to dna so what you're seeing here
seeing here isn't the whole e coli cell it's the e
isn't the whole e coli cell it's the e coli nucleoid it's the e coli dna
coli nucleoid it's the e coli dna what what this researcher had done was
what what this researcher had done was treat
treat their e coli cells with a fluorophore
their e coli cells with a fluorophore called dappy
called dappy dappy binds tightly to the e coli
dappy binds tightly to the e coli dna and what you're seeing here are all
dna and what you're seeing here are all of the
of the nucleoids for many different e coli
nucleoids for many different e coli glowing in blue
glowing in blue because dappy absorbs violet light and
because dappy absorbs violet light and it emits
it emits blue light now another type of
blue light now another type of microscopy that's
microscopy that's interesting it's a type of light
interesting it's a type of light microscopy but not a type we have
microscopy but not a type we have readily available to us in the lab is
readily available to us in the lab is differential
differential interference contrast or dic microscopy
interference contrast or dic microscopy this is an interesting type of
this is an interesting type of microscopy that uses a polarizer
microscopy that uses a polarizer to create two distinct beams of
to create two distinct beams of polarized
polarized light uh essentially light in a single
light uh essentially light in a single plane you know that
plane you know that light travels in different planes there
light travels in different planes there you got x y
you got x y axis you got um you know you've got the
axis you got um you know you've got the the
the the horizontal axis i should say in the
the horizontal axis i should say in the vertical axis
vertical axis you've got the vertical axis so
you've got the vertical axis so uh just like the little glasses you get
uh just like the little glasses you get at the 3d movies
at the 3d movies you know the gray glasses they give you
you know the gray glasses they give you for 3d movies
for 3d movies this eye gets different information than
this eye gets different information than this side because this side is getting
this side because this side is getting uh you know the the the vertical axis
uh you know the the the vertical axis polarized light this eyes getting
polarized light this eyes getting horizontal axis polarized light and then
horizontal axis polarized light and then you can see three-dimensional
you can see three-dimensional movies same concept applies here with
movies same concept applies here with dic microscopy
dic microscopy it uses these polarizers which gives you
it uses these polarizers which gives you know structures such as the nuclei
know structures such as the nuclei endospores vacuoles
endospores vacuoles inclusions a three-dimensional
inclusions a three-dimensional appearance so look at this
appearance so look at this here are those yeast cells under dic
here are those yeast cells under dic microscopy notice how they have this
microscopy notice how they have this this this 3d
this this 3d effect to them and it's because your
effect to them and it's because your eyeballs are getting different
eyeballs are getting different information now confocal scanning laser
information now confocal scanning laser microscopy this is another
microscopy this is another interesting form of microscopy that we
interesting form of microscopy that we don't have available to us in the lab
don't have available to us in the lab this takes the best of
this takes the best of dic and fluorescent microscopy and kind
dic and fluorescent microscopy and kind of puts them
of puts them together it takes
together it takes you it allows you to use lasers
you it allows you to use lasers to look at multiple sections
to look at multiple sections of a sample right and then feed that
of a sample right and then feed that information to a computer algorithm
information to a computer algorithm which then builds a three-dimensional
which then builds a three-dimensional model
model of those layers so essentially you're
of those layers so essentially you're using fluorescence microscopy
using fluorescence microscopy but by looking at a sliver of your
but by looking at a sliver of your sample at a time
sample at a time and then using computers to put all that
and then using computers to put all that information together and compile it into
information together and compile it into a three-dimensional image you get these
a three-dimensional image you get these beautiful
beautiful fluorescents three-dimensional images so
fluorescents three-dimensional images so you could look at for example a
you could look at for example a microbial community all together
microbial community all together and you could see that it clearly
and you could see that it clearly you can see what's going on in the
you can see what's going on in the in that community for instance a biofilm
in that community for instance a biofilm community
community now let's say you want to study a
now let's say you want to study a specimen that's tiny you want to study
specimen that's tiny you want to study a virus or you want to study the
a virus or you want to study the organelles inside of a
organelles inside of a cell you want to study individual
cell you want to study individual proteins
proteins now you're dealing in the realm of
now you're dealing in the realm of electron microscopy
electron microscopy so electron microscopes use electrons
so electron microscopes use electrons instead of visible light instead of
instead of visible light instead of the wavelengths member 300 to
the wavelengths member 300 to 700 we're talking about we're not we're
700 we're talking about we're not we're not using light at all we're using
not using light at all we're using the electrons which have a very small
the electrons which have a very small wavelength compared to that of
wavelength compared to that of visible light and this these these
visible light and this these these electrons are used to
electrons are used to image the cells to resolve the image
image the cells to resolve the image and instead of glass lenses which would
and instead of glass lenses which would just block the
just block the electrons we use electromagnets as
electrons we use electromagnets as lenses
lenses we have to operate these microscopes in
we have to operate these microscopes in a vacuum because
a vacuum because even air would block the electrons from
even air would block the electrons from you know doing their job a cam
you know doing their job a cam instead of looking through the
instead of looking through the microscope
microscope and seeing the specimen it's actually a
and seeing the specimen it's actually a photo sensor that receives that
photo sensor that receives that information so the electrons hit a photo
information so the electrons hit a photo sensor
sensor and that sensor sends the information to
and that sensor sends the information to a tele television screen
a tele television screen and there are two types you need to know
and there are two types you need to know about there are transmission
about there are transmission electron microscopes abbreviated tem
electron microscopes abbreviated tem microscopes
microscopes and scanning electron microscopes
and scanning electron microscopes abbreviated
abbreviated sem okay transmission electron
sem okay transmission electron microscopes
microscopes these have better resolution however
these have better resolution however you have to section your specimen you
you have to section your specimen you have to s
have to s you have to make slivers of your
you have to make slivers of your specimen and actually section it into
specimen and actually section it into tiny sections
tiny sections and you can see inside of the specimen
and you can see inside of the specimen where a scanning electron microscopy has
where a scanning electron microscopy has a little bit
a little bit a little bit worse resolution but
a little bit worse resolution but you can see the surface of specimens so
you can see the surface of specimens so if you want to look at the surface of
if you want to look at the surface of specimens
specimens you want sem if you want to see the
you want sem if you want to see the inside of
inside of sectioned and sliced specimens you're
sectioned and sliced specimens you're dealing t-e-m
dealing t-e-m so here is a tem microscope transmission
so here is a tem microscope transmission electron microscopy you could see
electron microscopy you could see at the top here you would have your
at the top here you would have your electron gun which is
electron gun which is essentially an electron source the
essentially an electron source the electrons radiate down
electrons radiate down through your specimen and
through your specimen and of course they have to go through a
of course they have to go through a evacuated chamber
evacuated chamber so it's a vacuum chamber and
so it's a vacuum chamber and the way the electrons get focused is by
the way the electrons get focused is by various electromagnets this is where you
various electromagnets this is where you stick your sample in
stick your sample in so the electrons cross strike your
so the electrons cross strike your sample
sample and go here to some kind of uh re
and go here to some kind of uh re you know receptor which then
you know receptor which then which then projects projects the
which then projects projects the information
information onto a screen here
now again with transmission electron microscopy you have
microscopy you have much greater resolving power 0.2
much greater resolving power 0.2 nanometers then light microscope look at
nanometers then light microscope look at this 0.2 nanometers
this 0.2 nanometers 0.2 nanometers that's ridiculous
0.2 nanometers that's ridiculous remember
remember a light microscope had the best
a light microscope had the best resolution at
resolution at 0.2 micrometers so
0.2 micrometers so uh think about 0.2 micrometers to 0.2
uh think about 0.2 micrometers to 0.2 nanometers about a thousand times
nanometers about a thousand times better than a light microscope
better than a light microscope right so a thousand times better resolve
right so a thousand times better resolve resolving power so you can see a
resolving power so you can see a thousand times better
thousand times better than the microscopes we have it in the
than the microscopes we have it in the lab
lab and you can see structures at the
and you can see structures at the molecular level you can see
molecular level you can see you can see individual molecules with
you can see individual molecules with with the
with the tem okay but again do you remember what
tem okay but again do you remember what i said
i said you have to section the samples very
you have to section the samples very thin
thin and we're talking 20 to 60 nanometer
and we're talking 20 to 60 nanometer sections
sections and and you can stain your specimen
and and you can stain your specimen you can stain it but you don't stain it
you can stain it but you don't stain it with dye
with dye like we do with light microscopy you
like we do with light microscopy you stain it with
stain it with high weight substances such as heavy
high weight substances such as heavy metals
metals right so silver or something
right so silver or something negative staining allows direct
negative staining allows direct observation of intex
observation of intex cells and components so you can either
cells and components so you can either stain
stain the specimen or you can stain the
the specimen or you can stain the background
background either way you're going to be able to
either way you're going to be able to have the contrast you need to see your
have the contrast you need to see your sample
sample so take a look here here's a few
so take a look here here's a few examples of tem
examples of tem actually it's one example
actually it's one example of tem two examples of tem one example
of tem two examples of tem one example of
of sem let me show you in a
sem let me show you in a you have a cell that is dividing
you have a cell that is dividing that is dividing you see this is a cell
that is dividing you see this is a cell with a septum
with a septum septum occurs during binary fission when
septum occurs during binary fission when a cell is dividing into two
a cell is dividing into two and you see this is a section of these
and you see this is a section of these two cells as they divide you can see the
two cells as they divide you can see the nucleoid here the nucleoid here
nucleoid here the nucleoid here the septum formed here this is a
the septum formed here this is a bacterial cell and look how much detail
bacterial cell and look how much detail you can see
you can see at this bacterial cell okay and then
at this bacterial cell okay and then here
here you can see this is actually a molecule
you can see this is actually a molecule it's a
it's a it's protein hemoglobin you know
it's protein hemoglobin you know hemoglobin the protein
hemoglobin the protein it's a quaternary structure so it's
it's a quaternary structure so it's actually several proteins working in
actually several proteins working in concert
concert but you can see the hemoglobin proteins
but you can see the hemoglobin proteins here
here with the negative staining what does
with the negative staining what does that mean the heavy metal is staining
that mean the heavy metal is staining the background
the background and the light colors which are not
and the light colors which are not stained are
stained are the hemoglobins and then in c
the hemoglobins and then in c we haven't touched on this yet but this
we haven't touched on this yet but this is a scanning electron micrograph
is a scanning electron micrograph of bacterial cells remember i said with
of bacterial cells remember i said with scanning electron microscopy
scanning electron microscopy you see the surface of cells so if
you see the surface of cells so if you're
you're ever seeing electron microscopy and you
ever seeing electron microscopy and you see
see surfaces like this you know it's a
surfaces like this you know it's a scanning electron micrograph
scanning electron micrograph if you're seeing inside of cells like
if you're seeing inside of cells like this you know it's a transmission
this you know it's a transmission electron micrograph
electron micrograph and just to show you that yes
and just to show you that yes researchers
researchers really do use all of these forms of
really do use all of these forms of microscopy
microscopy all of these images are from my own work
all of these images are from my own work when i was a graduate student a phd
when i was a graduate student a phd student at ut southwestern
student at ut southwestern and you can see i i had these mutant
and you can see i i had these mutant mice i was studying
mice i was studying and they're they're their pancreas
and they're they're their pancreas pancreas
pancreas was small did you know the plural of
was small did you know the plural of pancreas is pancreatic
pancreas is pancreatic you see this was a wild type or normal
you see this was a wild type or normal pancreas outlined in white
pancreas outlined in white of a mouse and then the mutant pancreas
of a mouse and then the mutant pancreas is is much stunted
is is much stunted in growth and much smaller so is the
in growth and much smaller so is the stomach but
stomach but here are the three mice the wild type
here are the three mice the wild type mouse heterozygous mouse and the mutant
mouse heterozygous mouse and the mutant mouse i was studying
mouse i was studying again this is a bright field image of
again this is a bright field image of the stomach
the stomach you can see the pancreas is large and
you can see the pancreas is large and in the mutants in the mutant stomach you
in the mutants in the mutant stomach you see the pancreas over here is quite
see the pancreas over here is quite small
small now with fluorescence microscopy i used
now with fluorescence microscopy i used a fluorophore called
a fluorophore called gfp green fluorescence protein
gfp green fluorescence protein that fluoresces green wherever the
that fluoresces green wherever the pancreas is you can see how big the
pancreas is you can see how big the pancreas is here
pancreas is here with fluorescence microscopy and see how
with fluorescence microscopy and see how small the pancreas is here
small the pancreas is here with the mutant with fluorescence
with the mutant with fluorescence microscopy i then sectioned
microscopy i then sectioned section the pancreatic and you could see
section the pancreatic and you could see that
that with this was bright field microscopy
with this was bright field microscopy with
with h e staining you can see the pancreatic
h e staining you can see the pancreatic bud of
bud of wild type wild type mouse
wild type wild type mouse pancreas and the mutant the mutant
pancreas and the mutant the mutant mouse pancreas and by the way these
mouse pancreas and by the way these pancreas are from the embryos not from
pancreas are from the embryos not from these mice here these are adult mice
these mice here these are adult mice these pancreata are from the embryos so
these pancreata are from the embryos so here you can see
here you can see the pancreatic bud is is developing
the pancreatic bud is is developing nicely
nicely in the in the wild type in the wild type
in the in the wild type in the wild type mouse but in the mutant mouse
mouse but in the mutant mouse it's not developing it's not growing and
it's not developing it's not growing and then i used uh
then i used uh phase contrast microscopy to look at the
phase contrast microscopy to look at the pancreatic bud
pancreatic bud as well to look at gene expression in
as well to look at gene expression in the pancreatic bud
the pancreatic bud and then i used confocal microscopy to
and then i used confocal microscopy to look at how the blood vessels are
look at how the blood vessels are forming see
forming see here i stained blood vessels red and you
here i stained blood vessels red and you could see the blood vessels are forming
could see the blood vessels are forming nicely in the
nicely in the in the wild type mouse but in the mutant
in the wild type mouse but in the mutant you can see that the dorsal pancreas is
you can see that the dorsal pancreas is not forming
not forming because the vascularization is not
because the vascularization is not developing correctly so you could see oh
developing correctly so you could see oh and and here again i also looked at
and and here again i also looked at insulin production in the pancreas
insulin production in the pancreas in the wild type mouse it's fine but in
in the wild type mouse it's fine but in the mutant mouse it was also fine so you
the mutant mouse it was also fine so you could see here
could see here all the different types of microscopy we
all the different types of microscopy we just talked about
just talked about maybe save the dic
maybe save the dic and darkfield but for the most part
and darkfield but for the most part researchers do use all the different
researchers do use all the different forms of microscopy
forms of microscopy in order to answer different types of
in order to answer different types of questions as they solve the riddles of
questions as they solve the riddles of life so
life so interesting stuff microscopy's always
interesting stuff microscopy's always been fascinating to me so hopefully you
been fascinating to me so hopefully you took away a little bit of information
took away a little bit of information there about
there about you know the types of microscopy and
you know the types of microscopy and where you would want to use
where you would want to use those for yourself now scanning electron
those for yourself now scanning electron microscopy remember what this is
microscopy remember what this is this is when you're looking at the
this is when you're looking at the surfaces of cells
surfaces of cells right and again you you your specimen
right and again you you your specimen is coated with a thin film of heavy
is coated with a thin film of heavy metal such as gold or silver
metal such as gold or silver and then an electron beam scans the
and then an electron beam scans the object
object it's an electron beam scans the surface
it's an electron beam scans the surface of the object and that relays that
of the object and that relays that information to a sensor
information to a sensor the scattered electrons are collected
the scattered electrons are collected and projected
and projected to produce an image and then even very
to produce an image and then even very large specimens can be observed because
large specimens can be observed because you're looking at scatter profiles
you're looking at scatter profiles and again the magnification isn't as
and again the magnification isn't as good as tem
good as tem but you can see the surface nicely
but you can see the surface nicely so now we're gonna hop into part three
so now we're gonna hop into part three of this chapter
of this chapter how microbial cultivation expands the
how microbial cultivation expands the horus horizon
horus horizon of my microbiology so
of my microbiology so what are the contributions of some of
what are the contributions of some of these early pioneers in
these early pioneers in microbiology but before we do so let's
microbiology but before we do so let's take another quick
take another quick break time with gizmo and wicket and
break time with gizmo and wicket and we'll come back to finish this chapter
we'll come back to finish this chapter hey everyone welcome back from break
hey everyone welcome back from break time with gizmo and wicked let's carry
time with gizmo and wicked let's carry on with this chapter
now here's some here's some uh concepts that i need you to know about this
that i need you to know about this concept of aseptic technique
concept of aseptic technique aseptic technique is a collection of
aseptic technique is a collection of practices that allows
practices that allows preparation and maintenance of sterile
preparation and maintenance of sterile chemicals
chemicals it's essentially how do i get my
it's essentially how do i get my bacteria from a culture
bacteria from a culture to a sterile medium in a way that
to a sterile medium in a way that minimizes the possibility of
minimizes the possibility of contamination
contamination and of course we learned aseptic
and of course we learned aseptic technique in the lab
technique in the lab remember that pure cultures are cells
remember that pure cultures are cells from
from only a single type of microorganism
only a single type of microorganism remember when a colony forms on a plate
remember when a colony forms on a plate that is an example of a pure culture
that is an example of a pure culture that is a clonal population
that is a clonal population if i were to take that colony from one
if i were to take that colony from one plate
plate and streak it onto another plate that is
and streak it onto another plate that is a pure culture of that colony
a pure culture of that colony enrichment culture techniques so isolate
enrichment culture techniques so isolate microbes having a particular metabolic
microbes having a particular metabolic characteristics from nature
characteristics from nature and early microbiologists
and early microbiologists had very important questions to answer
had very important questions to answer uh one being does spontaneous generation
uh one being does spontaneous generation occur spontaneous generation means
occur spontaneous generation means life spawning from nothing or life
life spawning from nothing or life spawning from dead material right
spawning from dead material right uh early on before the times of louis
uh early on before the times of louis pasteur
pasteur we as human we as humans believe that
we as human we as humans believe that spontaneous generation
spontaneous generation may be a viable explanation for life
may be a viable explanation for life that that
that that that life could come from a dead matter
that life could come from a dead matter and this answer uh was brought to you by
and this answer uh was brought to you by louis pasteur we're going to talk about
louis pasteur we're going to talk about louis pasteur and how he
louis pasteur and how he disproved this concept of spontaneous
disproved this concept of spontaneous generation
generation and two what is the nature of infectious
and two what is the nature of infectious disease
disease what infectious agents what which
what infectious agents what which specific bacteria are
specific bacteria are responsible for specific diseases this
responsible for specific diseases this was answered by
was answered by the postulates of robert koch
the postulates of robert koch all right so let's get started with
all right so let's get started with louis pasteur
louis pasteur louis pasteur was a chemist by training
louis pasteur was a chemist by training in fact
in fact vietnamese uh these are people who
vietnamese uh these are people who make wine hired him in order to
make wine hired him in order to understand better the process of
understand better the process of fermentation why was it that
fermentation why was it that their wines were you know that had
their wines were you know that had variable consistency at first it was
variable consistency at first it was thought that
thought that the process of fermentation and wine
the process of fermentation and wine making
making was simply a chemical process that
was simply a chemical process that occurs
occurs but with his investigation what he
but with his investigation what he what he realized essentially is that uh
what he realized essentially is that uh there is a biological element
there is a biological element fermentation is a biological process
fermentation is a biological process not strictly a chemical process and he
not strictly a chemical process and he developed
developed this whole idea behind yeast
this whole idea behind yeast being important for breaking down the
being important for breaking down the sugars
sugars in the wine making process in order to
in the wine making process in order to produce
produce the ethanol so he essentially discovered
the ethanol so he essentially discovered alcoholic fermentation and that led to a
alcoholic fermentation and that led to a revolution
revolution in wine making because now the
in wine making because now the vietnamese
vietnamese now they understood the importance of
now they understood the importance of adding yeast
adding yeast and having cultures of yeast present in
and having cultures of yeast present in their batches to make consistent
their batches to make consistent wine isn't that interesting and as i
wine isn't that interesting and as i mentioned before uh answering the
mentioned before uh answering the question of spontaneous generation that
question of spontaneous generation that life could spawn from
life could spawn from no life he used his famous
no life he used his famous uh swan neck technique
uh swan neck technique a swan neck flask technique to disprove
a swan neck flask technique to disprove spontaneous generation i'm going to show
spontaneous generation i'm going to show you how he did that in a slide coming up
you how he did that in a slide coming up and he was very instrumental in the
and he was very instrumental in the development of vaccines
development of vaccines he helped to develop the vaccine for
he helped to develop the vaccine for anthrax
anthrax cholera and rabies uh so
cholera and rabies uh so very very influential person also have
very very influential person also have you heard of pasteurization
you heard of pasteurization uh this is the process of taking uh
uh this is the process of taking uh a food that could spoil such as milk for
a food that could spoil such as milk for instance or beer
instance or beer raising the temperature sub boiling in
raising the temperature sub boiling in order to kill off
order to kill off most microorganisms and then cooling the
most microorganisms and then cooling the the
the liquid without spoiling the taste
liquid without spoiling the taste and uh you know that's that's
and uh you know that's that's responsible for
responsible for extending the shelf life of milk
extending the shelf life of milk right so how did uh how did pester's
right so how did uh how did pester's swan neck flask experiment work and how
swan neck flask experiment work and how did it disprove
did it disprove spontaneous generation so what you could
spontaneous generation so what you could see
see is if you take a non-sterile liquid
is if you take a non-sterile liquid and you pour it into a flask
and you pour it into a flask and then you heat the neck
and then you heat the neck of this of this flask into a
of this of this flask into a into a neck it's called the swan neck
into a neck it's called the swan neck then you you can sterilize
then you you can sterilize the liquid by extensive heating so
the liquid by extensive heating so extensive boiling
extensive boiling you can kill the microorganisms
you can kill the microorganisms in the liquid and the steam
in the liquid and the steam is expelled out of the open end
is expelled out of the open end now once you cool the liquid
now once you cool the liquid over time there the liquid remains
over time there the liquid remains sterile
sterile indefinitely so this this broth this
indefinitely so this this broth this this broth essentially uh
this broth essentially uh is it remains fresh right uh
is it remains fresh right uh it's not spoiled over a long period of
it's not spoiled over a long period of time
time and if you were to
and if you were to tip the flask or break
tip the flask or break the neck of the flask within a short
the neck of the flask within a short period of time
period of time the liquid becomes putrid uh it spoils
the liquid becomes putrid uh it spoils so what did this suggest to us
so what did this suggest to us it suggested that the the microorganisms
it suggested that the the microorganisms that were
that were spoiling the broth were not
spoiling the broth were not spawning out of the broth if they were
spawning out of the broth if they were spawning out of the broth
spawning out of the broth you know with spontaneous generation
you know with spontaneous generation then they should spawn here
then they should spawn here and they should spawn here in both of
and they should spawn here in both of these flasks
these flasks because air is able to get in and
because air is able to get in and air is required for life so you know
air is required for life so you know both of these should have spoiled
both of these should have spoiled however
however the reason this one didn't spoil is
the reason this one didn't spoil is because
because the dust which carries bacteria
the dust which carries bacteria the dust was collecting in the neck of
the dust was collecting in the neck of the flask
the flask so the the bacteria had no way to be
so the the bacteria had no way to be deposited onto the
deposited onto the liquid now here when you tip the flask
liquid now here when you tip the flask over
over or when you break the the neck of the
or when you break the the neck of the flask
flask the dust is able to settle that the dust
the dust is able to settle that the dust is able to get in and settle
is able to get in and settle and to spoil the the broth
and to spoil the the broth again this disproves spontaneous
again this disproves spontaneous generation
generation because it suggested that microbial
because it suggested that microbial contamination occurs from
contamination occurs from dust that's floating in the air it did
dust that's floating in the air it did not spawn
not spawn from the broth itself which is what
from the broth itself which is what people who believed spontaneous
people who believed spontaneous generation
generation thought all right another superstar in
thought all right another superstar in the field of microbiology another
the field of microbiology another founder of the field is robert koch a
founder of the field is robert koch a physician and microbiologist what he's
physician and microbiologist what he's best known for is establishing a link
best known for is establishing a link between
between specific microbes and the infectious
specific microbes and the infectious diseases that they cause this is
diseases that they cause this is done by his postulates his famous
done by his postulates his famous four postula it's known as cautious
four postula it's known as cautious postulates we're going to go over these
postulates we're going to go over these postulates and how they work
postulates and how they work but using conscious postulates you can
but using conscious postulates you can link
link a causative agent for a disease
a causative agent for a disease to the disease that's caused and by
to the disease that's caused and by using his postulates he was able to
using his postulates he was able to identify
identify the causative agent and by causative
the causative agent and by causative agent i mean the bacteria responsible
agent i mean the bacteria responsible for
for for instance for anthrax for
for instance for anthrax for tuberculosis for cholera
tuberculosis for cholera and i'm again i'm going to show you how
and i'm again i'm going to show you how he did this
he did this in a little bit but in addition to all
in a little bit but in addition to all that
that his laboratory was responsible for
his laboratory was responsible for developing
developing solid media for obtaining pure cultures
solid media for obtaining pure cultures of microbes
of microbes in fact you know the term petri dish or
in fact you know the term petri dish or petri plate
petri plate petri was a student was a member of
petri was a student was a member of koch's laboratory
koch's laboratory and also have you heard of agar you know
and also have you heard of agar you know agar plates
agar plates the agar was the idea of fanny hess the
the agar was the idea of fanny hess the wife of walter hess
wife of walter hess in koch's laboratory she suggested the
in koch's laboratory she suggested the use of
use of agar in plates so that it wouldn't
agar in plates so that it wouldn't be runny like gelatin because
be runny like gelatin because when people started culturing uh
when people started culturing uh bacteria they use things like potato
bacteria they use things like potato wedges
wedges like like they would cut a potato and
like like they would cut a potato and use that to grow bacterial colonies then
use that to grow bacterial colonies then they moved on to using
they moved on to using gelatin in the petri dish that wasn't
gelatin in the petri dish that wasn't very good because gelatin tends to be
very good because gelatin tends to be runny at 37 degrees
runny at 37 degrees and so it was fanny hess who suggested
and so it was fanny hess who suggested the use of agar
the use of agar in the petri dish and we've been using
in the petri dish and we've been using these techniques
these techniques all along us ever since we've been using
all along us ever since we've been using these techniques
these techniques develop in koch's lab so he was able to
develop in koch's lab so he was able to make the culture techniques
make the culture techniques and able to link diseases
and able to link diseases with the causative agents a very
with the causative agents a very interesting
interesting uh you know very interesting person
uh you know very interesting person very interesting times in lab and very
very interesting times in lab and very instrumental in
instrumental in launching microbiology as a field
launching microbiology as a field and for all of his efforts he was
and for all of his efforts he was awarded the nobel prize in physiology
awarded the nobel prize in physiology and medicine
so again what did he show us he developed ways to obtain pure cultures
developed ways to obtain pure cultures with aggro plates along with his
with aggro plates along with his associate
associate walter hess remember it was his wife who
walter hess remember it was his wife who suggested
suggested using agar walter has observed masses of
using agar walter has observed masses of cells called colonies now we know them
cells called colonies now we know them as clonal colonies
as clonal colonies and notice that these colonies have
and notice that these colonies have different shapes different colors
different shapes different colors different sizes
different sizes they started with those potato slices i
they started with those potato slices i told you about but then moved on to
told you about but then moved on to gelatin agar
gelatin agar it was richard petrie who devised the
it was richard petrie who devised the petri dish it was fanny hess
petri dish it was fanny hess who suggested the use of agar and we use
who suggested the use of agar and we use many many of these techniques today
many many of these techniques today so here's a picture of robert koch
so here's a picture of robert koch and again i told you i would mention his
and again i told you i would mention his four postulates and how he used the
four postulates and how he used the postulates
postulates in order to link a particular bacteria
in order to link a particular bacteria to a specific disease so what do you
to a specific disease so what do you have to do
have to do you find a diseased animal okay
you find a diseased animal okay a diseased animal let's say it has
a diseased animal let's say it has tell-tale signs of some disease
tell-tale signs of some disease and you want to figure out what bacteria
and you want to figure out what bacteria is causing that disease
is causing that disease well let's go to step one the suspected
well let's go to step one the suspected pathogen
pathogen must be present in all cases of the
must be present in all cases of the disease and
disease and absent from the healthy animal so what
absent from the healthy animal so what you would do
you would do is take a blood sample from this disease
is take a blood sample from this disease animal
animal and spread it on let's say a petri dish
and spread it on let's say a petri dish an agar
an agar petri dish you would then take a blood
petri dish you would then take a blood sample from a healthy animal
sample from a healthy animal and spread it on a dish as well
and spread it on a dish as well all right and this bacterial sample
all right and this bacterial sample this this this bacteria should only be
this this this bacteria should only be found in the diseased animal
found in the diseased animal but should be absent from healthy
but should be absent from healthy animals that's his first postulate the
animals that's his first postulate the second postulate
second postulate the suspected pathogen must be grown in
the suspected pathogen must be grown in pure culture so
pure culture so once you've once you've spread this on a
once you've once you've spread this on a plate you pick that colony you spread
plate you pick that colony you spread you streak that on a plate
you streak that on a plate and you find individual colonies you
and you find individual colonies you isolate the
isolate the the bacteria from this deceased animal
the bacteria from this deceased animal you isolate that individual colony
you isolate that individual colony um and you streak out that colony on a
um and you streak out that colony on a plate you have to be able to do that
plate you have to be able to do that and of course you you should not be able
and of course you you should not be able to find that bacteria
to find that bacteria from the healthy animal number three
from the healthy animal number three the cells from a pure culture from this
the cells from a pure culture from this pure culture
pure culture you have to inject them into
you have to inject them into healthy animals and those healthy
healthy animals and those healthy animals need to become
animals need to become diseased so what did you do you took
diseased so what did you do you took some of these
some of these health these uh colonies from you know
health these uh colonies from you know that you
that you that you harvested from this original
that you harvested from this original animal
animal you take this bacteria and you inoculate
you take this bacteria and you inoculate a
a healthy animal with the suspected
healthy animal with the suspected pathogen does that make sense so you
pathogen does that make sense so you have to be able to take the bacteria
have to be able to take the bacteria that you
that you isolated from the original animal
isolated from the original animal inoculate
inoculate a healthy animal and that healthy animal
a healthy animal and that healthy animal has to
has to succumb to the same disease it has to
succumb to the same disease it has to present the same disease as the original
present the same disease as the original and then as a final step you have to
and then as a final step you have to again be able to re-isolate the original
again be able to re-isolate the original bacteria so you have to take blood from
bacteria so you have to take blood from this
this deceased animal again and be able to
deceased animal again and be able to find that bacterium again
find that bacterium again and theoretically you should be able to
and theoretically you should be able to do this over and over again you should
do this over and over again you should be able to do
be able to do this exact same procedure over and over
this exact same procedure over and over again
again the mouse dies of a disease you take the
the mouse dies of a disease you take the blood you isolate the bacteria
blood you isolate the bacteria you inject that into a healthy animal it
you inject that into a healthy animal it dies
dies you can then retrieve the the blood
you can then retrieve the the blood again
again find that colony again inject that
find that colony again inject that colony again
colony again and the di and the mouse dies again so
and the di and the mouse dies again so you should be able to repeat this over
you should be able to repeat this over and over again and that establishes a
and over again and that establishes a link
link between that specific bacteria that
between that specific bacteria that species of bacteria
species of bacteria and the disease that it caused right and
and the disease that it caused right and by doing so
by doing so he was able to identify the causative
he was able to identify the causative agents for several diseases
agents for several diseases now i should mention that
now i should mention that the efforts of koch really
the efforts of koch really solidified the germ theory of infectious
solidified the germ theory of infectious disease
disease that germs these microorganisms are
that germs these microorganisms are responsible for for infectious disease
responsible for for infectious disease this was
this was highly debated at the time at the late
highly debated at the time at the late mid to late 1800s it was
mid to late 1800s it was not known it was not experimentally
not known it was not experimentally shown that germs cause communicable
shown that germs cause communicable diseases
diseases infectious diseases it was really robert
infectious diseases it was really robert koch who
koch who showed that demonstrated real link
showed that demonstrated real link between
between microbes and infectious diseases with
microbes and infectious diseases with his postulates
his postulates before that see before that it was
before that see before that it was suspected that they caused disease but
suspected that they caused disease but no direct proof
no direct proof and the people who showed indirect proof
and the people who showed indirect proof early on
early on uh before the time of koch was where
uh before the time of koch was where ignez
ignez samuelweiss and joseph lister let me
samuelweiss and joseph lister let me tell you about these very interesting
tell you about these very interesting people
people uh ignis samuelweiss was a hungarian
uh ignis samuelweiss was a hungarian physician
physician and he promoted hand washing and when he
and he promoted hand washing and when he promoted hand washing
promoted hand washing this was uh revolutionary
this was uh revolutionary especially in the pediatric wards during
especially in the pediatric wards during uh you know post uh maternity when
uh you know post uh maternity when when when moms would give birth right uh
when when moms would give birth right uh he would
he would he would say okay we need to wash our
he would say okay we need to wash our hands and when when
hands and when when when doctors wash their hands during the
when doctors wash their hands during the process this lead to decrease
process this lead to decrease mortality of infants after
mortality of infants after you know after they were born but again
you know after they were born but again he was ridiculed by his colleagues
he was ridiculed by his colleagues because his colleagues really didn't
because his colleagues really didn't believe
believe in germ theory of disease they thought
in germ theory of disease they thought he was just superstitious
he was just superstitious and even though he showed much better
and even though he showed much better survival he showed that these
survival he showed that these children are surviving better and people
children are surviving better and people are surviving better
are surviving better after hand washing he was ridiculed
after hand washing he was ridiculed eventually driving him to depression he
eventually driving him to depression he was committed to an asylum
was committed to an asylum and he was eventually beaten to death
and he was eventually beaten to death by guards isn't that a sad story so
by guards isn't that a sad story so ignorance saml wise
ignorance saml wise you know really was important
you know really was important early figure in sanitation in the
early figure in sanitation in the hospital setting and it was
hospital setting and it was just a terrible story here of his own
just a terrible story here of his own colleagues
colleagues uh ridiculing him when he was ahead of
uh ridiculing him when he was ahead of his time
his time joseph lister he was a surgeon and he
joseph lister he was a surgeon and he was the first to sterilize his surgical
was the first to sterilize his surgical instruments before
instruments before operating so what he would do instead of
operating so what he would do instead of just
just hacking off a limb you know with a saw a
hacking off a limb you know with a saw a rusty saw
rusty saw he would uh treat the area
he would uh treat the area with phenol a very powerful disinfectant
with phenol a very powerful disinfectant and he would also treat his surgical
and he would also treat his surgical instruments with phenol
instruments with phenol in fact phenol is a steroid and then
in fact phenol is a steroid and then this led to
this led to improvements in recovery and minimized
improvements in recovery and minimized post-operative infection so he was the
post-operative infection so he was the first
first surgeon to sterilize his
surgeon to sterilize his equipment his surgical instruments
equipment his surgical instruments but again all of these were indirect
but again all of these were indirect evidence of the germ theory of disease
evidence of the germ theory of disease it wasn't until
it wasn't until koch came along linking a particular
koch came along linking a particular causative agent to a disease
causative agent to a disease that we really started getting concrete
that we really started getting concrete answers as to what causes disease
answers as to what causes disease another pioneer in the field martinez
another pioneer in the field martinez bayern of dutch origin he was able to
bayern of dutch origin he was able to develop
develop enrichment culture techniques that we
enrichment culture techniques that we use
use to to to now to today
to to to now to today this involves isolating
this involves isolating microbes with a highly selective media
microbes with a highly selective media by
by manipulating the nutrients in the media
manipulating the nutrients in the media and the incubation conditions
and the incubation conditions he was also instrumental in describing
he was also instrumental in describing viruses
viruses by discovering that viruses
by discovering that viruses cause uh disease uh in and he
cause uh disease uh in and he he linked the tobacco mosaic virus
he linked the tobacco mosaic virus to tobacco mosaic disease
to tobacco mosaic disease another pioneer sergey weinogradski
another pioneer sergey weinogradski of russian origin he
of russian origin he discovered chemolithotropes these are
discovered chemolithotropes these are these
these uh earth eaters these are microorganisms
uh earth eaters these are microorganisms that are
that are able to break down different types of
able to break down different types of molecules for for energy this this
molecules for for energy this this chemolithotrophy
chemolithotrophy oxidation of inorganic compounds to
oxidation of inorganic compounds to yield energy
yield energy very interesting stuff and we'll talk
very interesting stuff and we'll talk about chemolithotrophy in a in a chapter
about chemolithotrophy in a in a chapter to come
all right so with that that leads us to the end of chapter one
the end of chapter one quite a long chapter but then again
quite a long chapter but then again we're introducing an entire field here
we're introducing an entire field here of microbiology very interesting stuff
of microbiology very interesting stuff please let me know in the comments below
please let me know in the comments below if you have any questions
if you have any questions and i will catch you guys next time
dr d dr d dr d dr d dr d dr d a dr d dr d
dr d dr d a dr d dr d dr dr
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