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00:01 Welcome folks for those of you listening this recorded lecture that were in class

00:07 the day of this lecture, which been last this past Thursday, 25

00:14 this is gonna sound slightly different to because it's not the live lecture,

00:18 stupidly forgot to initiate the recorder. uh so I'm doing this on

00:26 so but anyway, I will cover obviously covering the same content and I

00:32 give the same lecture on the slides you saw, so and try

00:37 you know, have pretty much duplicate I did thursday. So um

00:42 so let's go and get started. um if you just didn't roll in

00:47 course, remember that all course material on blackboard. Okay, so do

00:53 look through everything on black on the course site, There's lots of

00:57 they're not everything visible yet, but know, you will start beginning to

01:01 quizzes pop up, starting next later next week, another material,

01:07 you have everything you need for, know, one which are electric

01:11 etcetera. So again, just and the and schedules of everything are posted

01:17 there in front of the blackboard, make sure you are aware of what's

01:21 up, what to do etcetera. . Uh if you just enrolled either

01:26 or today, you'll you'll have access within a day or so, I

01:33 send you a copy of the syllabus you want me to do that,

01:35 email me lastly, uh remember we're we're using the clicker if you have

01:42 uh you're using your clickers, I've posting questions. Did so this week

01:47 both both lecturers will next week as . Uh Remember right now doesn't count

01:53 anything really. The purpose is to reassure yourself that you're using your

02:00 clicker points are being recorded and you're your points on blackboard. So that's

02:05 of what this period here is about to make sure that your everything's working

02:10 more or less and you're seeing your . I will um upload the points

02:15 friday from this past week. I some on for Tuesday session but I'll

02:20 it again today as people are entering their clickers and entering the course I'm

02:25 to constantly refresh the turning point So you should see your points,

02:32 been using a clicker and it's registered should be seeing your points uh appear

02:38 if you don't then that's a red that something is not right. So

02:40 would check with the clicker support people campus. Okay? Anyway so uh

02:49 more thing so with the mobile app I that I encourage people to use

02:52 mobile app it's cheap. It's a option. It's on your cell phone

02:56 you know people don't normally forget their when they come to class. So

03:01 that's why I recommend unless of course have the handheld version from previous semester

03:06 certainly but in any case there was couple of questions last time about when

03:11 entered the session I. D. is what you want to do.

03:14 you see the little diagram there so always want to enter the session

03:18 D. Changes every class. If have the hand held clicker the channel

03:23 is for you that number is always same. But those with the mobile

03:27 the session I. D. Always . So you just punch this in

03:31 the mobile app. Uh You may a user I. D.

03:35 just ignore it. You don't need do anything. They're just join the

03:39 and you're good. Okay so if have a registered clicker you're fine because

03:43 will tie into your name and your as points are uploaded to blackboard.

03:49 . All right that's enough for the stuff so you'll notice. So today

03:54 gonna we're gonna go through begin going chapter one. We've got uh two

03:59 to cover this so we'll finish this next Tuesday. And um uh so

04:05 go through roughly have have a little material in this session. So a

04:11 of things you'll you'll see that if haven't already you'll see that each of

04:15 lecture notes at the beginning have a learning objectives. Okay this is basically

04:24 this as a but as when you've the chapter what should you know about

04:31 ? These are kind of a list things that you should that you should

04:34 . Okay so take it kind of in that way. And so

04:38 every all lecture notes for every our habits in front to kind of

04:42 it as a guide to, you if you to these bullet points that

04:48 understand, what is that, what's described there? Okay. Alright.

04:53 we started we started the session with yet. Sorry. So chapter one

04:59 . So I just made a This is covering chapter one and we'll

05:02 through uh we didn't quite reach all way down to here, so we'll

05:10 get through most of that and then the rest for later. So here's

05:14 we started uh so we have clicker we started the session with we have

05:18 three in a row here. Obviously can't answer them at home. So

05:24 while the question was up the point . So in this first chapter uh

05:28 really go to microbiology and intro to really and to describe really to define

05:36 they are, who are they, are the representative types? Uh taxonomic

05:41 what groups are they in? Um also kind of to emphasize the benefit

05:49 microbes. And yes of course uh of course microbes have gotten a negative

06:00 . And so uh it's just to you that that's those types of cause

06:05 are really in the vast minority. majority of microbes uh uh if not

06:13 , they don't really harm anything, they most have some kind of uh

06:18 niche that benefits us in some Okay, as this kind of meant

06:22 point out some of those things. if you look at this question,

06:26 false answer is actually c okay, looking for the false statement here.

06:33 uh that's false because they provide much than that they provide. Actually.

06:39 not, it's not a value you to memorize but just Show you why

06:44 incorrect. 50% or more. So of course, are due to um

06:51 types, your algae, your um environment will be allergy, which of

07:00 the diet on things like that, also a significant portion are also cyanobacteria

07:05 are pro carry a photosynthetic organisms. um in fact, ancestral types of

07:13 bacterial photo synthesizers that produce oxygen uh ancestors from to about three billion years

07:21 , 2 to 3 billion years ago the ones that put oxygen in the

07:24 atmosphere. So um obviously a major . It's what then you allowed an

07:31 using metabolism to evolve. Um and uh appear at the top microbes are

07:38 . This is this is a term that you always see associated with microbes

07:42 they are literally found almost everywhere on planet. Um whether in extreme environments

07:49 as very cold. You see down , it's from the North Pole um

07:55 uh Yellowstone park. And you see guys are up here in that

08:01 Very hot water obviously uh there are that can grow a handful of soil

08:07 you see here contains bazillions of microbes various types eukaryotic probe periodic Et

08:14 Okay so um the the uh statement of microbes taken 90% of nitrogen at

08:25 75%. That's part of that's the cycle. Very critical that you see

08:29 here are very critical um process um for life on this planet because um

08:41 you think of the whole the basic food chains and trophic levels we call

08:46 uh in ecosystems. Um Bottom wrong most abundant are the producers.

08:54 Your plants and terrestrial environments. Uh other photosynthetic types of marine environments as

09:01 as they are. They only need and CO. Two and water for

09:05 most part they can't manufacture their own . So they require nitrogen phosphorus.

09:11 think of agricultural areas where they're growing plants need to provide fertilizer in the

09:18 of nitrogen and uh prosperous. And um so the nitrogen cycle provides those

09:28 that's and there's numerous reactions to the election cycle producing various usable products.

09:36 products that can be used I think all driven by different types of

09:41 Um The and the processes of notification . We'll talk about these later on

09:49 a very critical cycle because these minerals for producers for the synthetic types and

09:57 that of course provides food for those consumers. Right? So urban

10:03 other levels of consumers. So it's critical to life on this planet.

10:08 as well as other types of minerals are cycled like phosphorous for example.

10:13 these are all many of these are to heavily due to bacterial uh types

10:18 activity. Okay. Um Cultural So the statement in e. Is

10:24 of course. Um The numbers of out there that are out there in

10:27 environment, we've barely been able to We've only been able to take uh

10:34 cultivate these in the lab to grow and isolate them. Only a very

10:38 small portion because we don't know, don't know all of the the types

10:43 nutrients that may be needed, support . Um So there is a vast

10:49 are not able to be cultured for . There is a way to actually

10:52 identify those that we can't go on . And we'll mention that uh in

10:56 little while. Um uh But the there is, you know, there's

11:01 many different nutritional types and interactions between and the environment. Some supply nutrients

11:07 others. Uh And so there's all of what we call feeding relationships and

11:11 don't have figured out for many what is that actual requirement to grow them

11:16 the lab. So Uh this organism causes syphilis to this date is still

11:20 able to be grown. We've known this organism since early 1900s and still

11:24 not yet been able to grow in lab. So there are these kinds

11:28 things that happened. Um and then point about microbes, our microbiome,

11:35 ? The microbes in and on our , our number our own selves by

11:42 of magnitude. So uh microbes been this deep longest living members that have

11:52 around more than anybody else are And they've been here since, followed

11:56 Archaea. They've been on this planet more than three billion years. Um

12:02 relatively recent. Our human evolution began six million years ago. And of

12:08 microbes were along not that you know they're a part of us and they

12:16 influenced us in terms of our immune , uh nutrients they can provide for

12:21 and many other many other things. very critical. And so um our

12:27 is very important as well from a of standpoints. So um and so

12:34 down here uh this said the This is the central dogma, one

12:41 the universal concepts in biology. The of the flow of information occurs.

12:45 just to point out that microbes have the model for really studying lots of

12:51 basic processes. Uh We learned uh molecule of inheritance being D.

12:57 A. The mechanism of protein the mechanisms of DNA replication um the

13:05 code and what that represents all these of basic fundamental processes uh were figured

13:11 using uh really bacterian viruses as the for this because they're easy to grow

13:16 work with and manipulate. So again very important on all in many different

13:22 . Okay. Are are microbes? um there's another question. So this

13:27 asks you know they've been around for long. Pro carrots have been,

13:36 history goes back farther than any other form on this planet. So why

13:39 they so successful? Right. This to why they're so highly adaptable.

13:43 so this is asking what is the why I prepared? So how do

13:48 adapt? Why not? What is ? What is not a reason why

13:51 are so highly adaptable. And of the answer there is D.

13:55 Circled E. N. G. a different reason. But this is

13:58 correct answer because that's false. Precarious carry out sexual reproduction. They are

14:05 reproduce a binary fission. And the there is is that okay if they

14:10 by binary fission they're basically making genetic identical copies. How they how do

14:16 introduce variation in the population? So . Right evolution. 101.

14:21 You have to have it's all about . Right? Survival and reproduction.

14:27 ? So if you're one is surviving presumably um they have the most favorable

14:34 of genes for that particular environment and that they produce more offspring. And

14:41 genes are perpetuated. Okay so that's the in basic terms the mechanism

14:48 Okay and so um so variation is critical to that. So genetic variation

14:56 um survived. So if a if condition environmental conditions change in some way

15:06 more variation in the population means there be a subset in that population that

15:12 the right combination of genius to to better survive that particular condition. So

15:18 if everybody wore clones of each other everybody would succeed or fail similarly.

15:26 . But so genetic variation is very in us and other eukaryotes, it's

15:31 to sexual reproduction. Right? And mutation Korea and archaea can't do that

15:40 reproduce sexually. They they have other . So they do have higher mutation

15:45 . Uh It's what's called a spontaneous right? Don't worry about that

15:49 But you know they don't but don't that to mean they mutate crazy out

15:54 control. Uh But like a virus viruses can mutate rather quickly because there's

16:01 checks on repairing their mistakes. But there are mechanisms to prepare mistakes but

16:07 with that they still just have a like 111 in six million won in

16:16 of the one in a million is of a spontaneous mutation rate. One

16:19 is not fixed for every million. So um But you couple that mutation

16:28 uh with a very fast growth Okay and so uh and that fast

16:37 rate is due to having small genomes small size. Right? So E

16:42 G. Actually correlates A. Because enable fast growth to occur in small

16:48 not as much cytoplasm material to keep with small genome to copy and then

16:52 ability to transcribe and translate. So that's that part of that process of

16:58 of information. Right? You transcribe . N. A. Uh you

17:03 the so DNA transcribing RNA. And is translated into protein. And so

17:11 fast growth requires to have lots of synthesis. And when you can have

17:17 two processes occurring virtually at the same that allows you to make lots of

17:21 which can support fast growth. Uh that can only happen because there's no

17:27 membrane. So there's no separation of processes and ourselves and other eukaryotes,

17:33 nuclear membranes separates those two processes. they can occur together. So again

17:39 enable contribute to why they can grow fast and so fast growth rate means

17:44 evolution is all about reproduction. And so you can introduce the mutation

17:50 very quickly they can produce 20 generations You know in some cases 8-10

17:56 Uh it would take us 400 years to produce that many generations. So

18:01 can uh you know a very quick uh beneficial or not. That will

18:08 seen uh because the number of generations so quickly. You can see if

18:13 beneficial if it's not on the So uh that goes to why

18:19 It's can be so highly adaptable as as the fact that they have diverse

18:23 capabilities. Right? So able to function survive in various environments um and

18:30 know be ubiquitous as we've mentioned because these diverse capabilities. So this all

18:36 to why they've been so successful. so this is kind of segue us

18:42 kind of the definition. So remember this in this uh chapter kind of

18:47 about defining microbes what types of microbes are? And this kind of goes

18:50 that question. And so the answer which we consider a microbe is gonna

18:55 . Um Only one correct here is Okay monkey pox virus viruses are considered

19:02 . Okay um D. And Are multicellular animals. Although super

19:10 We don't consider those microbes. Microbes um uh uni sailor unique cellular

19:19 Typically they can be in arrangements or types of arrangements in groups but um

19:26 course the hallmark is you have to have to be able to see what

19:28 microscope. But you know it's it's uni cellular life. Um It's not

19:35 animals. And that's what the target is what's called a water bear

19:39 Of course is an insight. These multicellular animals. Skin tissue. So

19:43 skin tissue for example any kind of these are organs these are not even

19:48 cells making those tissues organs up are . Um Those are meant cells are

19:56 to function as part of a of group. I mean they can't really

20:03 independently on their own. Uh They very specific requirements. Uh They are

20:09 what to do. Typically buy signals off by that animal or plant.

20:16 Hormonal signals, things of that type tell ourselves to grow or not and

20:19 have you. So we don't consider microorganisms. Okay, B. And

20:24 . In a similar vein um Although matter of green algae or biofilm

20:30 represents a a large accumulation of Okay, so if they can grow

20:38 to such a high mass they can visible to the naked eye. As

20:42 a colony on a plate. So colony starts with a single cell that

20:46 and divides after several hours. So cells are present that it becomes visible

20:50 the naked eye. So the colony , you don't consider a microbe.

20:54 biofilm is not considered micro but of the entities making those each up would

20:59 a microbe. Okay, so again there's gonna be some of these um

21:05 on on the microbe definition. so I'm sure you know, you

21:10 obviously requires a microscope to be observed you're defining microbe typically uh sailor entities

21:17 there's an asterisk because viruses are not . Okay but we do consider those

21:22 . Uh They're not multicellular types. not multicellular animals in time. And

21:28 cells, cellular types of microbes, of course have features that other cells

21:33 , but they typically live independently. can have arrangements. So especially for

21:40 and archaea. Uh they can have changed. It can be clusters,

21:45 can be filament, so it expands morphology. Okay. Um and so

21:53 wise, you see the size of here. So it'd be good to

21:57 kind of the average range of each . Right? Your eukaryotes and prokaryotes

22:01 viruses. Okay, so 20 and is simply your eukaryotic cells and

22:09 1 to 10 microns. Or procure less than one micron virus is the

22:15 limit is around .2 microns. Uh that I think believe rabies virus

22:25 is on that lower in the tobacco virus. But regardless there is,

22:29 is a very tiny viruses. Typically need to have a electron microscope.

22:37 . Okay. Um of course there's be some a little bit of

22:41 There can be eukaryotic microbes that may a little under 20 microbes. Some

22:45 carrots can get bigger. Uh so there's a little bit of variation between

22:50 trees. Kind of basically average we see. Okay, in terms

22:53 a lower limit on size. So here you see a flu

22:57 So the lower limit is gonna be in um around here for virus.

23:04 , that's around 20 mike nanometers. so you begin to run into turn

23:09 the fact that um the size of molecules themselves can be a limitation.

23:14 you can only get to us so of a small size. Okay.

23:19 and and it won't work. So that's why viruses really are comprised

23:23 a lot. Because there's not enough to accommodate having a lot of structures

23:27 sign it. Okay, They're basically a protein sack surrounding a genome.

23:32 ? There are some variations. But small size means that they can't really

23:37 a lot of stuff in there, that's not what viruses are about.

23:41 . So if we go um to upper limit and we'll talk about that

23:45 a in a second here. The limit, Right, There are factors

23:50 limit how big a cell can get well. Okay, um and I'll

23:56 that shortly. So who are the ? Well, we can divide it

24:01 sailor and a sailor. Okay. so cellular based life. So your

24:07 and pro Teesta, which would be like eastern molds for fungi. Pro

24:12 algae, protozoa wins and the bacteria archaea. So this differentiates between prokaryotes

24:20 eukaryotes. Right, So fungi, are eukaryotic microbes, eukaryotic micro

24:26 Uh so I'm sure you're aware of archaea and bacteria I'm sure you're familiar

24:34 the basic differences between these two Uh pro carry oats. Of

24:40 the hallmark. There is lacking the state, like organelles. Typically uh

24:44 circuit of chromosome etcetera. Okay, . Archaea the members of that

24:51 And that's the other thing that there's groups of pro cario. There's the

24:55 and the archaea. Um Archaea often extremophiles although they can find them at

25:01 temperatures, right? We actually have of archaea in our bodies, but

25:06 can be found also in extreme environments extremes of temperature and other physical

25:12 Um So you carry out uh as know, this nucleus multiple linear chromosomes

25:21 can reproduce either sexually or a sexually on the type. So, you

25:26 features I'm sure you're already aware of the a cellular side. In terms

25:30 microbes, we have viruses, viruses prions. Okay, so viruses comprised

25:35 protein nucleic acids. Uh Vai roids prions are unique in that one.

25:44 viral loads are basically infectious RNA viruses typically only uh an issue for plants

25:51 is today, there is no known infected by virus roids or anything other

25:55 plants. Certain types, we'll talk that later. But crayons, there

26:01 your familiarity is like the mad cow . That's a prion disease. It's

26:05 infectious protein. Right? So for and prions, it's RNA, viral

26:11 prions and that's the only structures associated it. Okay. Nothing else.

26:17 very unique. Um Okay, so just a word on archaea that uh

26:27 can be grouped into three different loosely grouped into. So if you

26:34 anarchy a typically fits one of these categories while or halo file.

26:43 And some of the characteristics of these thermal files. And you know with

26:47 Kia it's it's very common to in vicinity find bacteria as well.

26:53 So don't think that archaea live by . They are certainly uh in uh

27:00 by side with bacteria because bacteria can thermal files as well. It's just

27:04 archaea tend to be on the upper of these extremes. So for

27:08 hyper thermal files. Right? So what we call upper levels of temperature

27:14 our for these archaea are in the and 10 range hypothermia files we call

27:20 that are 80 degrees and above. , I'm showing here Um bacterial thermal

27:27 are typically in like the 450-70 There can be some differences but don't

27:33 too hung up on that. Uh can be of course aerobic anaerobic

27:38 different types of sulfur metabolize ear's are this group. Again, we'll mention

27:44 things later in the semester. Um jen's. So whereas you can have

27:49 bacteria and archaea thermal files only Archaea are method Mogens. Okay. And

27:55 of course that's the production of methane is a greenhouse gas. Um It's

27:59 anaerobic process. It's very sensitive to . Um found in cows are probably

28:08 number one source of methane and of it's the the archaea method genic archaea

28:15 are in them that produce it. You can't you can't have some combinations

28:20 these features. So you can have pathogens can be thermal files. So

28:24 can it's not unusual to have combinations these features. Um And of course

28:30 also find tangents and in landfills uh treatment plants as well. Uh So

28:40 we'll mention methodologies later in the Halo files of course are salt

28:45 Right? So they go in extreme conditions. Uh These are conditions you

28:50 like say there's some natural bodies of . They're very salty, like the

28:54 sea and great salt lake. Uh are come from manufacturers of sodium

29:01 So they'll take seawater, put them these shallow pools, water evaporates.

29:05 you have a very uh concentrated salt . And that's where these bacteria can

29:11 grow in. Um They do have unusual photos and photosynthetic type. They're

29:16 chlorophyll based. So your familiarity is with plants and algae that photosynthesize.

29:22 you have oxygen and using chlorophyll as pigment. Uh These are very

29:28 They're actually the light absorbing pigments are analogous to retinal. That's in our

29:35 . So very unusual, but a primitive thought to be very predating chlorophyll

29:41 photosynthesis. Um Anyway and so like said, we'll touch on on these

29:47 in the semester, but just to you an idea of what the archaea

29:51 about. Uh viruses as mentioned. of course these are a sailor.

29:57 require a host. And so the is always, are they alive or

30:00 ? Right. And so viruses you don't know you have a viral,

30:05 affected by the virus until you show of some type of disease.

30:09 Um viruses can reside outside of a . And that brings up the question

30:14 in that state, are they alive dead? Because they're not reproducing but

30:19 they may still be viable and by . I mean you can have a

30:23 hanging out on a door knob for . And it's not replicating of course

30:28 the kind of state is that in it could be dead, so to

30:32 . So what that would mean is no longer infectious? It can't even

30:35 a host were around, it wouldn't able to infect because it's no longer

30:39 . But it could just be kind viable in that you touch a door

30:44 and you infect yourself. And it then find its host and begin replicating

30:49 that cell. So the viability of outside their host varies depending on the

30:54 type, environmental conditions etcetera. So I think it's been documented that

31:00 can last can remain viable outside the for days if not a couple of

31:06 . So uh so it just depends time. But again the hallmark with

31:10 is they they because they're small and don't carry a lot of material with

31:15 . They rely on a host for like protein synthesis, replication of the

31:21 etcetera. Okay, so again, expand on viruses later on. Um

31:28 what we call a sailor type of variations on the microbe concept.

31:35 so um the uh so this thing this as kind of uh maybe outliers

31:51 maybe, you know, features that not necessarily outliers. But you

31:54 there's there's there's always in biology, everything, not everything always fits in

31:59 nice neat box. Right? There's lots of gray areas where you have

32:03 that don't exactly fit the the So um it's just something you

32:10 Right? And so many times maybe forms or something. But you

32:15 there are there are variations of the concept definition. So super sized cells

32:21 one of those. So there's this called margarita magnificat to in fact that

32:27 , this genius style margarita is one contains these very large bacterial types.

32:33 all similar that they have a they sulfur as an energy source.

32:39 But they come in different forms. all of them tend to be kind

32:42 a large size so large. You see them with the naked eye.

32:46 millimeters is something that's the centimeters. you can see that with your naked

32:49 . You see the filament over there the right is one of those uh

32:53 certain algal species that can be certain fungal species uh here's a bubble

32:59 . You see there that's quite It's often called sea grapes is another

33:05 , but they are um that's a cell and they're unusual and that that

33:11 cell is actually made up of multiple is what we call multi nuclear.

33:15 we've actually popped. That bubble nuclei go flying. They'll colonize them growing

33:20 another bubble. So it's actually a to spread them if they're if they're

33:23 popped. Okay. Um the microbial so visible to the naked eye.

33:31 we mentioned this in the question So you can have um uh biofilms

33:38 are a an aggregation, a proliferation millions of cells. Okay, biofilm

33:46 . We'll talk about that as well in the semester. This it's a

33:49 specific phenomenon. Uh It's a gene phenomenon. It's just not it's not

33:54 random just coming together cells. It's it's an orchestrated process, but biofilms

34:00 all about surface. So biofilms begin a surface and then can get so

34:05 that they not only grow two dimensionally the surface but three dimensionally off the

34:10 . And so you see that plugged pipe there representing a tremendous amount of

34:15 growth. So you can find biofilms water pipes uh different types of

34:20 Um So while that massive growth means can see with the naked eye of

34:27 to see the individual microbes, you to have a microscope. So,

34:30 know, microbes can come together to a structure visible to the naked eye

34:35 similarly with a colony on a Okay, then we mentioned already micro

34:40 are multicellular animals. We don't consider microbes. Okay, so kind of

34:44 to this, we talked about the end um the lower end limit on

34:51 , you know, that the size molecules themselves can limit how small an

34:55 can be a cell can be. here's kind of the other spectrum.

34:59 it's too large. Right? One the things uh so have to deal

35:05 , is that um surface to volume . Right? So as you get

35:11 or get bigger, rather right, surface to volume ratio gets smaller as

35:21 go get bigger. Okay. Remember exchange with the environment. Right.

35:27 in the exchange across the membrane. if the surface of iron ratio has

35:30 down, that makes it harder to to be able to fulfill the requirements

35:34 the self to get enough material in out. Okay. And so as

35:39 , diffusion can be an issue. , molecules uh in a in a

35:45 said, is all uh need to able to travel right to get to

35:49 if it's a substrate to get their enzyme. So to um so as

35:55 it still gets larger, that can a problem, you carry out to

35:58 around that by by compartmentalizing specific molecules to transport them transport vesicles through a

36:09 through the cytoplasm that there's always you do this because their large size but

36:15 don't have those properties. So uh without a margarita, you see

36:20 here's a cross section of one of of its filament structure, right?

36:25 so big, right? It's filled nitrate. It's what it does

36:29 It has nitrate and it has sulfur here, right? The yellow

36:35 And so it actually uses sulfur Like H. Two S.

36:39 Or S. O. Could be sulfur. And it can use those

36:43 an energy source. Right? Supplying transport chain. And then can we

36:49 would use oxygen and reduce that water in our respiratory system. But they

36:54 use nitrate. Right? And use and reduce it to nitrite.

36:58 Remember this is what fuels a TP , right? Remember your mitochondrial in

37:03 mitochondria, right? You use things glucose. Right? And you use

37:08 to breathe. And then the as result you produce lots of a

37:12 They so they do a little They use hydrogen sulfide or other types

37:16 sulfur compounds oxidize those and then uh reduce nitrite to nitrate nitrate to

37:25 And they can produce their energy that in the form of A.

37:28 P. S. Okay. So so having a large section of their

37:34 body filled with nitrate gives them a they store sulfur and nitrate this way

37:40 that if they're if they're food limited have a source of energy with them

37:44 all times. And so but then do you supply the needs of the

37:49 so big? Well they've had this way of of compartmentalizing in these what

37:55 called Pepin's. Right These structures are to carry out um protein synthesis.

38:02 they compartmentalize that in these structures all the cell body length so it can

38:10 the needs of that single cell. it's waiting around that diffusion issue by

38:15 what it needs in different locations So it's it's again it's just you

38:19 need I'm not gonna test you on margarita but just the example to show

38:23 how something this big can can survive by adapting in this way. Okay

38:31 um now you know these supersized cells the bacterial types of microbes are like

38:39 aren't necessarily the majority. So if look at most you know bacteria or

38:45 and have you most you're gonna be the what you call quote normal size

38:49 . But you are gonna have some are gonna be in these areas where

38:54 what we call super sized cells and is how they are able to survive

38:57 adapt to those conditions. Okay so the microbial family tree. Okay so

39:07 of course you with all life. like to classify it classify life.

39:14 . And uh with microbes of course been done with in variety of ways

39:27 the biochemical tests. So you basically anything is about. Okay, what

39:34 the similarities and differences? Okay. in history taxonomy that's taken on different

39:40 . Right. Initially all you can do is look at the observable features

39:45 you know there's more features in common not then they're more closely related,

39:49 them together. Then if there's not many similarities that later went on to

39:56 with microbes at least a was to a microscope to see them and then

40:02 that there are different types of shapes sizes of microbes. Then later on

40:07 capabilities. What can they do and do in terms of their biochemistry and

40:12 ? Okay, so that was for longest time how classification of microbes

40:18 Uh then along came of course uh discovery of D. N.

40:23 And the ability to isolate D. . A. And look at the

40:27 of D. N. A. remember that you know when you're comparing

40:30 sequences right? D. N. . Is a G. C.

40:34 . These bases that each one is a point of difference. So you're

40:38 at 10,000 Based sequence of DNA. are 10,000 differences. So you're looking

40:44 how many of these how many of are similar in the same position.

40:48 gives you an idea of how related not related they are. Okay,

40:53 you can't use the species definition as done with you carry outs,

40:58 Because it relies on sexual reproduction. , uh members are members of a

41:04 are part of the same species if only breed within that group,

41:08 doesn't fit with microbes. So we to use these other um, ways

41:13 to uh describe them. Okay, uh we look at a brief taxonomic

41:21 . It all hinges really, of on the microscope and development and advances

41:26 microscopy. Okay, so initially really , you know, going back to

41:33 ancient Greece things are classified as either , vegetable or mineral. Okay.

41:41 and so with, with microbes of , uh they're either lumped into animal

41:46 plant kingdom. If it was a like photosynthetic, it would be of

41:49 lumped into the plant kingdom. If didn't have that property would be considered

41:54 animal. But strangely enough, what now know is fungi or actually were

42:00 in the kingdom. Plant type likely they have. If you look at

42:03 on the plant, they have kind like a root like system to some

42:07 , but fungi are actually closely more related to us than they are to

42:11 , algae, of course makes sense they're photosynthetic. Um but then along

42:17 heckle uh late 18 hundreds, 18 and uh takes all the microbes out

42:29 the animal plant kingdom and put them a kingdom called pro Teesta. And

42:33 protease that he had like six or different groups within pro Teesta representing different

42:39 of microbes. And one of those was actually manera. And so Montero's

42:44 became the pro carry abs. And so he he classified microbes in

42:52 if they really lack any kind of structure. So as we look at

42:56 if you look at a a cell he saw that there's really no discernible

43:00 inside of it, like a nucleus something that he said, well this

43:03 just protoplasm and that's it. I'm I'm gonna put these guys in

43:08 And so later on, particularly when electron microscope was developed, you can

43:13 see differences between eukaryotic and procure erotic nucleus or no nucleus, organelles,

43:18 cetera. And so then that became Manero contained precarious. So that then

43:25 distinguishing between pro carry it. You out so many arrows All pro carry

43:29 . Pro Teesta algae and protozoa ones of course in pro Teesta uh because

43:37 eukaryotic cells, uh fungi yeasts and of course the eukaryotic. So again

43:45 terms of microbes, so you're gonna microbes in kingdom fungi yeasts and

43:49 Pro Teesta algae and protozoa wins and precarious. Okay. And so of

43:55 the big advancement then was was um uh archaea bacteria that there was actually

44:05 pro cariocas, within manera, there actually two groups of precarious and that

44:10 significant. Okay and so what was this was a group of carl woes

44:18 George fox. And that's George fox in the U. H. About

44:23 department. Uh They both worked to look at these pro carriers that seem

44:30 be in occupy these extreme environments. so using a hard to cultivate.

44:38 they tried then to to isolate the . N. A. And what

44:42 picked the molecule for reference uh which the ribosomes. Okay so if you're

44:49 to um and so if you're familiar the tree of life this is what's

44:53 going on for several decades now is classify all life on this planet and

45:00 do so um to see to examine relationships and so forth. But they

45:07 this this particular DNA sequence which is sequence that codes for the 16

45:13 RNA molecules. So remember all the genes DNA codes for a protein.

45:20 are types that the end product is itself and these are gonna be

45:25 Is associated with ribosomes. RNA. are that make up transfer RNA is

45:30 you remember that from protein synthesis. um the of the robot RNA is

45:36 16 S. Was chosen because it's of intermediate size. It's about 1500

45:42 pairs long. So it's relatively quick easy to sequence. Okay um and

45:49 it's kind of a corny analogy maybe think think of if you wanted to

45:55 the evolution of um of transportation, ? Taking out, taking it away

46:02 science for a bit, but you to describe the evolution of transportation,

46:07 might go, okay, what's common not all, but most forms of

46:11 , and you might guess the wheel around the wheel would have been around

46:16 a long time. First to you know, as a car to

46:20 materials and a car to transport humans the back of the horse, then

46:26 , then uh, into locomotive and , um, then of course

46:33 etcetera. So it was a long there. So, the point

46:36 you could basically use the wheel to way back in time to trace the

46:40 of transportation and how it evolved. , and you couldn't make a lot

46:45 changes to a wheel without really affecting function, right? You wouldn't want

46:49 have if you ungrounded the wheels, to speak, and make it very

46:53 to use. So you couldn't make lot of changes to a wheel,

46:57 that's kind of analogous to the Okay, so, of course,

47:01 living things have arrived, zone all cell based life ribosomes that we

47:07 of and uh, arriving some something you can't make a lot of mutations

47:13 over, over millennia. Right? because it would affect the ability to

47:19 proteins and of course, that's a function. If you can't do that

47:23 species becomes extinct. So so it's way to really go back in time

47:27 examine all life. Okay this And so um if we look at

47:36 16 S. So again we're looking the D. N. A.

47:39 codes for the 16 S. And the 16. That simply means

47:42 S. Number and S values all meat refers to with a mass the

47:47 . So a bigger number S is Svedberg units. Um It has to

47:53 with centrifuge components and you get a . So the point is a big

47:58 a big s value is a big . Right? So the uh we're

48:03 at the so we compare the DNA that codes for that 16 S.

48:08 . Okay. And so you can the actual 16 S. RNA of

48:13 bacteria and archaea because what was found actually you see a difference between within

48:19 group of pro periods. You see difference between these two. Okay.

48:22 two distinct groups and sort of bacteria the archaea. And so the arrows

48:28 see are the areas where changes occur that's what's used for comparison.

48:36 And so the other parts of molecules really amenable to changes without completely altering

48:43 function. Okay so the arrows that see pointing out that's where the what

48:48 call hotspots occur, where changes that occur here. Okay and so that's

48:53 used for comparison. And so um so with this work, you

48:57 there was this what was come up what's called the three domain system.

49:02 . And so you carry out, the equivalent to the 16 S.

49:07 in eukaryotes is what's called the 18 . RNA. Okay, so those

49:13 the 18 S RNA would be classified um you carry those. So you

49:20 domain, you Kariya. And so I'm under bacteria Archaea. They all

49:25 a distinct difference between those 16 RNA sequences. So uh significant.

49:30 basically broken up into the domains bacteria archaea. Uh of course you carry

49:37 animal kingdom, plant kingdom, fungi protease to of course. So um

49:43 significant in terms of, you two groups of precarious. Okay.

49:49 so uh there you see the three and then we look unusual about archaea

49:54 they're they're deaf. Make no they're definitely precarious but they because they

50:00 lack the nucleus, they black they have those precarious features for

50:08 Along with diverse metabolism, small circular etcetera. But unlike bacteria, Archaea

50:14 similarities to eukaryotes, particularly in terms some of their informational molecules like those

50:20 involved in transcription, like RNA polymerase with that eukaryotes, uh some of

50:28 mechanisms of protein synthesis, somewhere similar to eukaryotes. Uh if you may

50:33 may not recall the the gene structure the UK RIO has that in intron

50:43 structure. And there's some areas that that at least on some of their

50:47 . So again just showing kind of you carry as compared to bacteria that

50:54 don't have those similarities to you So for that reason it's kind of

50:59 that that in terms of ancestral right common ancestor of all of all three

51:08 , that bacteria evolved first and then you carry uh anarchy. Uh Anyway

51:18 so um so so obviously the ability sequence is based on you know being

51:26 to isolate and work with the So microbial genomes obviously like all genomes

51:32 uh show the capabilities, you know what it's capable of various genes involved

51:38 utilizing the organism for various functions uh with any uh and then you prepare

51:47 you're gonna have um you know, shared by all. So for example

51:52 all of course have e. Coli our systems. Um and but now

51:58 the coal is going to be Of course you're going to be what

52:01 call variant strains of E coli uh coli that cause you know the because

52:07 outbreak in terms of food borne illness such as chipotle and other restaurants associated

52:13 tainted produce. Typically That's a new called 157 uh pathogen. Then there's

52:20 course your basic benign lab e coli uh cole i B K. 12

52:30 are e coli is because they they're by having these are called core genes

52:35 genes involved in informational processes that are whether you're a pathogen or not but

52:42 them as nico. And but then have of course certainly the 157 would

52:47 genes that relate to its ability to disease that the lab strain would

52:50 So you're gonna have differences like But because bacteria easily grown as well

52:56 archaea and have a small chromosome we seek in these sequences very quickly and

53:02 for identification purposes as well. Many purposes for this. And one of

53:07 is this meta genome some meta So what that is this this is

53:13 allows a survey called. We can culture very we've only cultured a very

53:19 portion of what's actually out there in of microbes we can find what's out

53:23 without culturing them by using meta Okay so what you and I have

53:28 slide here to show uh that so have you can have an environmental

53:33 It can be uh water, sediment, what have you whatever.

53:39 what you're doing is you're taking that and you're not trying to grow

53:43 What you're gonna do is just isolate total D. N. A.

53:47 that sample. So you just basically all the D. N.

53:50 Of all the cells in that Okay then you're gonna do some common

53:55 . N. A. Work by cutting up the DNA fragments cloning them

54:01 vectors. Okay and then putting them cells. So e coli is often

54:08 for this purpose. And so the cells will contain in in these

54:13 They're holding all the fragments of all D. N. A. That

54:18 in that sample. Okay so you have a library of all these DNA

54:23 you isolated from your sample up Okay. Or now in that

54:30 Okay and you can use that to maybe unique types of proteins. You

54:35 you can have those cells express those and and then study the proteins that

54:41 produce. Um you can set up conditions to analyze activities of these things

54:48 of course there's a wide application in industry. Maybe finding new kinds of

54:53 , other antiviral drugs etcetera. Uh can you can you can find you

55:00 use this for biotechnology if you certainly to commercialize a particular type of protein

55:05 may have found that has a unique activity. What have you uh microbial

55:11 . Right? You can you can , you can do the sequencing of

55:14 fragments and compare it to databases online sequenced organisms. And from in the

55:22 of microbial ecology you can um take samples and see what's actually out

55:28 What's what are the micro regions that coexisting together what's their metabolic functions and

55:34 are they doing? So this this is very powerful allows you to do

55:38 all without having to try to culture again, you're not gonna from the

55:45 you take, you're only gonna be the culture a very tiny fraction of

55:48 in there. So this allows you expand and really find out what's actually

55:53 there. Okay, it's a very tool. And so um so we

55:59 of segue then a little bit into in human history. So certainly uh

56:06 a historical perspective, my chronology begins they when they become discovered. But

56:11 course before then unknowingly basically we've used for certainly for food production, beer

56:19 wine productions were going on for Okay. And obviously unknowingly as

56:25 they've caused infectious diseases that have decimated population, the world's population at various

56:30 whether the plague, smallpox etcetera. . So discover, of course as

56:38 you've heard through this discussion, you , we've used them for all kinds

56:41 things. Um the benefit, you , for our benefit and for basic

56:47 etcetera. Okay, so when we at um uh discovery of microbes,

57:01 , these two individuals hook and then one hook. Okay. And

57:10 There is Hook produced the first microscope was one that was very low

57:17 So when he actually viewed weren't what he viewed were uh either whole

57:23 uh tissues. Um macroscopic organisms basically he was look at them and see

57:32 they're comprised of. He was actually first person to coin the term

57:36 Okay. But he again he wasn't really at microbes, his Van labor

57:42 a hook that was able to produce microscope. And that's although very odd

57:49 . That is a microscope with a that was able to produce around 300

57:55 . Magnification. Which is quite remarkable the time. And certainly that will

57:59 you to see very tiny entities such bacteria which you see in the drawings

58:04 . So he's kind of credited with the and he called him animal

58:08 but being kind of the father of for that reason. So um and

58:13 course the discovery of microbes opened up invisible world that hadn't been seen

58:19 Okay. And so uh this this of spontaneous generation, right? A

58:28 life from non life okay, have an idea that's been around for centuries

58:33 . And microbes kind of come into microbes kind of then gives more fuel

58:41 the people that believed in spontaneous generation terms of that they thought microbes could

58:47 from non life. Because before that of course thought all life could this

58:52 happen with. But ready was kind the one to show that okay,

58:59 life, more complex forms of this couldn't happen. And this experiment

59:03 of essentially refuted that so you have remember that during this time, you

59:07 , we're talking all kinds of crazy were around this time, um that

59:13 could, you know, if you an open grain, open grain

59:18 you rats running around. And so idea was, okay, grain grain

59:23 to rats. Uh so all kinds crazy beliefs like this. And

59:29 uh you see a meat carcass hanging a butcher shop, right? And

59:32 see flies around, there's no refrigeration then. So you see flies hovering

59:37 , and then all of a sudden see maggots appear in the meat.

59:39 the maggots are spontaneously arising from the meat. No, not true.

59:45 already really, this proved that by , you know, here's the first

59:49 . And we see flies completely open . Of course flies are able to

59:55 in. And you see maggots appear if you have a cork sealed

59:59 nothing can get in the meat does produce maggots. And then so the

60:04 here was the people that believe in generation. They they're thing was that

60:11 most matter can can produce life, you must have air present,

60:18 What they call the vital force. has to be present. Okay,

60:22 that's the reason for having this flask . Gauze allows air to come

60:28 So they fulfill the criteria that air allowed to be present, but still

60:33 wouldn't form because flies weren't allowed to . So it's the flies laying the

60:37 that give rise to the maggots, not spontaneous generation. And so then

60:43 kind of most people dancing. Say, okay, well,

60:47 spontaneous generation can occur cannot occur with organisms. But describe your microbes as

60:53 said, give them more fuel and , okay, well, it can

60:56 with microbes because if you have a and you leave it open and all

61:01 a sudden cells appear in it. ? And so you see the spellings

61:04 experiment here where ross and again, just like a nutrient broth, growth

61:11 that sustain themselves, that if you it sterilize it, let it cool

61:16 you kept it open, more than would occur. And that's that was

61:21 them that was proof of spontaneous But then if you heated it and

61:25 sealed the flask, well then no occurred. Okay, but again,

61:30 kind of back to this argument up , Right? You have to have

61:34 in there. So the spontaneous the that were pro spontaneous generation said,

61:39 , that that doesn't work because you're allowing air to get in.

61:43 that's why I'm not getting growth air have spontaneous generation. So that current

61:48 not enough to convince anybody that spontaneous wasn't a thing to allow microbes to

61:53 . Okay, so this is then when uh passenger comes in.

61:58 that's actually where I stopped on uh . So that's where we'll pick it

62:05 and we'll get into um uh finishing past your medical microbiology and a little

62:12 about ecology. Okay, so that's , folks. I'll and I'll post

62:17 lecture, so we will see you time. The next one of these

62:20 be live, so I'm not gonna not to turn the recorder on.

62:24 , thanks, folks,

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