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00:01 | Welcome folks for those of you listening this recorded lecture that were in class |
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00:07 | the day of this lecture, which been last this past Thursday, 25 |
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00:14 | this is gonna sound slightly different to because it's not the live lecture, |
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00:18 | stupidly forgot to initiate the recorder. uh so I'm doing this on |
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00:26 | so but anyway, I will cover obviously covering the same content and I |
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00:32 | give the same lecture on the slides you saw, so and try |
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00:37 | you know, have pretty much duplicate I did thursday. So um |
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00:42 | so let's go and get started. um if you just didn't roll in |
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00:47 | course, remember that all course material on blackboard. Okay, so do |
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00:53 | look through everything on black on the course site, There's lots of |
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00:57 | they're not everything visible yet, but know, you will start beginning to |
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01:01 | quizzes pop up, starting next later next week, another material, |
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01:07 | you have everything you need for, know, one which are electric |
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01:11 | etcetera. So again, just and the and schedules of everything are posted |
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01:17 | there in front of the blackboard, make sure you are aware of what's |
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01:21 | up, what to do etcetera. . Uh if you just enrolled either |
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01:26 | or today, you'll you'll have access within a day or so, I |
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01:33 | send you a copy of the syllabus you want me to do that, |
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01:35 | email me lastly, uh remember we're we're using the clicker if you have |
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01:42 | uh you're using your clickers, I've posting questions. Did so this week |
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01:47 | both both lecturers will next week as . Uh Remember right now doesn't count |
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01:53 | anything really. The purpose is to reassure yourself that you're using your |
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02:00 | clicker points are being recorded and you're your points on blackboard. So that's |
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02:05 | of what this period here is about to make sure that your everything's working |
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02:10 | more or less and you're seeing your . I will um upload the points |
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02:15 | friday from this past week. I some on for Tuesday session but I'll |
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02:20 | it again today as people are entering their clickers and entering the course I'm |
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02:25 | to constantly refresh the turning point So you should see your points, |
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02:32 | been using a clicker and it's registered should be seeing your points uh appear |
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02:38 | if you don't then that's a red that something is not right. So |
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02:40 | would check with the clicker support people campus. Okay? Anyway so uh |
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02:49 | more thing so with the mobile app I that I encourage people to use |
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02:52 | mobile app it's cheap. It's a option. It's on your cell phone |
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02:56 | you know people don't normally forget their when they come to class. So |
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03:01 | that's why I recommend unless of course have the handheld version from previous semester |
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03:06 | certainly but in any case there was couple of questions last time about when |
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03:11 | entered the session I. D. is what you want to do. |
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03:14 | you see the little diagram there so always want to enter the session |
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03:18 | D. Changes every class. If have the hand held clicker the channel |
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03:23 | is for you that number is always same. But those with the mobile |
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03:27 | the session I. D. Always . So you just punch this in |
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03:31 | the mobile app. Uh You may a user I. D. |
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03:35 | just ignore it. You don't need do anything. They're just join the |
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03:39 | and you're good. Okay so if have a registered clicker you're fine because |
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03:43 | will tie into your name and your as points are uploaded to blackboard. |
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03:49 | . All right that's enough for the stuff so you'll notice. So today |
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03:54 | gonna we're gonna go through begin going chapter one. We've got uh two |
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03:59 | to cover this so we'll finish this next Tuesday. And um uh so |
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04:05 | go through roughly have have a little material in this session. So a |
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04:11 | of things you'll you'll see that if haven't already you'll see that each of |
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04:15 | lecture notes at the beginning have a learning objectives. Okay this is basically |
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04:24 | this as a but as when you've the chapter what should you know about |
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04:31 | ? These are kind of a list things that you should that you should |
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04:34 | . Okay so take it kind of in that way. And so |
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04:38 | every all lecture notes for every our habits in front to kind of |
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04:42 | it as a guide to, you if you to these bullet points that |
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04:48 | understand, what is that, what's described there? Okay. Alright. |
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04:53 | we started we started the session with yet. Sorry. So chapter one |
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04:59 | . So I just made a This is covering chapter one and we'll |
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05:02 | through uh we didn't quite reach all way down to here, so we'll |
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05:10 | get through most of that and then the rest for later. So here's |
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05:14 | we started uh so we have clicker we started the session with we have |
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05:18 | three in a row here. Obviously can't answer them at home. So |
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05:24 | while the question was up the point . So in this first chapter uh |
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05:28 | really go to microbiology and intro to really and to describe really to define |
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05:36 | they are, who are they, are the representative types? Uh taxonomic |
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05:41 | what groups are they in? Um also kind of to emphasize the benefit |
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05:49 | microbes. And yes of course uh of course microbes have gotten a negative |
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06:00 | . And so uh it's just to you that that's those types of cause |
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06:05 | are really in the vast minority. majority of microbes uh uh if not |
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06:13 | , they don't really harm anything, they most have some kind of uh |
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06:18 | niche that benefits us in some Okay, as this kind of meant |
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06:22 | point out some of those things. if you look at this question, |
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06:26 | false answer is actually c okay, looking for the false statement here. |
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06:33 | uh that's false because they provide much than that they provide. Actually. |
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06:39 | not, it's not a value you to memorize but just Show you why |
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06:44 | incorrect. 50% or more. So of course, are due to um |
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06:51 | types, your algae, your um environment will be allergy, which of |
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07:00 | the diet on things like that, also a significant portion are also cyanobacteria |
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07:05 | are pro carry a photosynthetic organisms. um in fact, ancestral types of |
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07:13 | bacterial photo synthesizers that produce oxygen uh ancestors from to about three billion years |
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07:21 | , 2 to 3 billion years ago the ones that put oxygen in the |
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07:24 | atmosphere. So um obviously a major . It's what then you allowed an |
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07:31 | using metabolism to evolve. Um and uh appear at the top microbes are |
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07:38 | . This is this is a term that you always see associated with microbes |
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07:42 | they are literally found almost everywhere on planet. Um whether in extreme environments |
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07:49 | as very cold. You see down , it's from the North Pole um |
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07:55 | uh Yellowstone park. And you see guys are up here in that |
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08:01 | Very hot water obviously uh there are that can grow a handful of soil |
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08:07 | you see here contains bazillions of microbes various types eukaryotic probe periodic Et |
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08:14 | Okay so um the the uh statement of microbes taken 90% of nitrogen at |
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08:25 | 75%. That's part of that's the cycle. Very critical that you see |
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08:29 | here are very critical um process um for life on this planet because um |
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08:41 | you think of the whole the basic food chains and trophic levels we call |
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08:46 | uh in ecosystems. Um Bottom wrong most abundant are the producers. |
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08:54 | Your plants and terrestrial environments. Uh other photosynthetic types of marine environments as |
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09:01 | as they are. They only need and CO. Two and water for |
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09:05 | most part they can't manufacture their own . So they require nitrogen phosphorus. |
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09:11 | think of agricultural areas where they're growing plants need to provide fertilizer in the |
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09:18 | of nitrogen and uh prosperous. And um so the nitrogen cycle provides those |
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09:28 | that's and there's numerous reactions to the election cycle producing various usable products. |
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09:36 | products that can be used I think all driven by different types of |
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09:41 | Um The and the processes of notification . We'll talk about these later on |
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09:49 | a very critical cycle because these minerals for producers for the synthetic types and |
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09:57 | that of course provides food for those consumers. Right? So urban |
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10:03 | other levels of consumers. So it's critical to life on this planet. |
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10:08 | as well as other types of minerals are cycled like phosphorous for example. |
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10:13 | these are all many of these are to heavily due to bacterial uh types |
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10:18 | activity. Okay. Um Cultural So the statement in e. Is |
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10:24 | of course. Um The numbers of out there that are out there in |
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10:27 | environment, we've barely been able to We've only been able to take uh |
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10:34 | cultivate these in the lab to grow and isolate them. Only a very |
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10:38 | small portion because we don't know, don't know all of the the types |
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10:43 | nutrients that may be needed, support . Um So there is a vast |
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10:49 | are not able to be cultured for . There is a way to actually |
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10:52 | identify those that we can't go on . And we'll mention that uh in |
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10:56 | little while. Um uh But the there is, you know, there's |
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11:01 | many different nutritional types and interactions between and the environment. Some supply nutrients |
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11:07 | others. Uh And so there's all of what we call feeding relationships and |
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11:11 | don't have figured out for many what is that actual requirement to grow them |
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11:16 | the lab. So Uh this organism causes syphilis to this date is still |
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11:20 | able to be grown. We've known this organism since early 1900s and still |
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11:24 | not yet been able to grow in lab. So there are these kinds |
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11:28 | things that happened. Um and then point about microbes, our microbiome, |
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11:35 | ? The microbes in and on our , our number our own selves by |
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11:42 | of magnitude. So uh microbes been this deep longest living members that have |
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11:52 | around more than anybody else are And they've been here since, followed |
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11:56 | Archaea. They've been on this planet more than three billion years. Um |
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12:02 | relatively recent. Our human evolution began six million years ago. And of |
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12:08 | microbes were along not that you know they're a part of us and they |
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12:16 | influenced us in terms of our immune , uh nutrients they can provide for |
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12:21 | and many other many other things. very critical. And so um our |
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12:27 | is very important as well from a of standpoints. So um and so |
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12:34 | down here uh this said the This is the central dogma, one |
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12:41 | the universal concepts in biology. The of the flow of information occurs. |
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12:45 | just to point out that microbes have the model for really studying lots of |
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12:51 | basic processes. Uh We learned uh molecule of inheritance being D. |
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12:57 | A. The mechanism of protein the mechanisms of DNA replication um the |
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13:05 | code and what that represents all these of basic fundamental processes uh were figured |
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13:11 | using uh really bacterian viruses as the for this because they're easy to grow |
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13:16 | work with and manipulate. So again very important on all in many different |
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13:22 | . Okay. Are are microbes? um there's another question. So this |
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13:27 | asks you know they've been around for long. Pro carrots have been, |
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13:36 | history goes back farther than any other form on this planet. So why |
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13:39 | they so successful? Right. This to why they're so highly adaptable. |
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13:43 | so this is asking what is the why I prepared? So how do |
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13:48 | adapt? Why not? What is ? What is not a reason why |
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13:51 | are so highly adaptable. And of the answer there is D. |
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13:55 | Circled E. N. G. a different reason. But this is |
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13:58 | correct answer because that's false. Precarious carry out sexual reproduction. They are |
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14:05 | reproduce a binary fission. And the there is is that okay if they |
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14:10 | by binary fission they're basically making genetic identical copies. How they how do |
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14:16 | introduce variation in the population? So . Right evolution. 101. |
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14:21 | You have to have it's all about . Right? Survival and reproduction. |
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14:27 | ? So if you're one is surviving presumably um they have the most favorable |
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14:34 | of genes for that particular environment and that they produce more offspring. And |
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14:41 | genes are perpetuated. Okay so that's the in basic terms the mechanism |
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14:48 | Okay and so um so variation is critical to that. So genetic variation |
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14:56 | um survived. So if a if condition environmental conditions change in some way |
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15:06 | more variation in the population means there be a subset in that population that |
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15:12 | the right combination of genius to to better survive that particular condition. So |
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15:18 | if everybody wore clones of each other everybody would succeed or fail similarly. |
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15:26 | . But so genetic variation is very in us and other eukaryotes, it's |
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15:31 | to sexual reproduction. Right? And mutation Korea and archaea can't do that |
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15:40 | reproduce sexually. They they have other . So they do have higher mutation |
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15:45 | . Uh It's what's called a spontaneous right? Don't worry about that |
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15:49 | But you know they don't but don't that to mean they mutate crazy out |
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15:54 | control. Uh But like a virus viruses can mutate rather quickly because there's |
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16:01 | checks on repairing their mistakes. But there are mechanisms to prepare mistakes but |
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16:07 | with that they still just have a like 111 in six million won in |
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16:16 | of the one in a million is of a spontaneous mutation rate. One |
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16:19 | is not fixed for every million. So um But you couple that mutation |
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16:28 | uh with a very fast growth Okay and so uh and that fast |
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16:37 | rate is due to having small genomes small size. Right? So E |
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16:42 | G. Actually correlates A. Because enable fast growth to occur in small |
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16:48 | not as much cytoplasm material to keep with small genome to copy and then |
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16:52 | ability to transcribe and translate. So that's that part of that process of |
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16:58 | of information. Right? You transcribe . N. A. Uh you |
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17:03 | the so DNA transcribing RNA. And is translated into protein. And so |
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17:11 | fast growth requires to have lots of synthesis. And when you can have |
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17:17 | two processes occurring virtually at the same that allows you to make lots of |
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17:21 | which can support fast growth. Uh that can only happen because there's no |
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17:27 | membrane. So there's no separation of processes and ourselves and other eukaryotes, |
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17:33 | nuclear membranes separates those two processes. they can occur together. So again |
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17:39 | enable contribute to why they can grow fast and so fast growth rate means |
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17:44 | evolution is all about reproduction. And so you can introduce the mutation |
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17:50 | very quickly they can produce 20 generations You know in some cases 8-10 |
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17:56 | Uh it would take us 400 years to produce that many generations. So |
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18:01 | can uh you know a very quick uh beneficial or not. That will |
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18:08 | seen uh because the number of generations so quickly. You can see if |
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18:13 | beneficial if it's not on the So uh that goes to why |
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18:19 | It's can be so highly adaptable as as the fact that they have diverse |
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18:23 | capabilities. Right? So able to function survive in various environments um and |
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18:30 | know be ubiquitous as we've mentioned because these diverse capabilities. So this all |
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18:36 | to why they've been so successful. so this is kind of segue us |
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18:42 | kind of the definition. So remember this in this uh chapter kind of |
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18:47 | about defining microbes what types of microbes are? And this kind of goes |
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18:50 | that question. And so the answer which we consider a microbe is gonna |
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18:55 | . Um Only one correct here is Okay monkey pox virus viruses are considered |
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19:02 | . Okay um D. And Are multicellular animals. Although super |
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19:10 | We don't consider those microbes. Microbes um uh uni sailor unique cellular |
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19:19 | Typically they can be in arrangements or types of arrangements in groups but um |
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19:26 | course the hallmark is you have to have to be able to see what |
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19:28 | microscope. But you know it's it's uni cellular life. Um It's not |
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19:35 | animals. And that's what the target is what's called a water bear |
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19:39 | Of course is an insight. These multicellular animals. Skin tissue. So |
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19:43 | skin tissue for example any kind of these are organs these are not even |
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19:48 | cells making those tissues organs up are . Um Those are meant cells are |
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19:56 | to function as part of a of group. I mean they can't really |
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20:03 | independently on their own. Uh They very specific requirements. Uh They are |
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20:09 | what to do. Typically buy signals off by that animal or plant. |
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20:16 | Hormonal signals, things of that type tell ourselves to grow or not and |
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20:19 | have you. So we don't consider microorganisms. Okay, B. And |
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20:24 | . In a similar vein um Although matter of green algae or biofilm |
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20:30 | represents a a large accumulation of Okay, so if they can grow |
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20:38 | to such a high mass they can visible to the naked eye. As |
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20:42 | a colony on a plate. So colony starts with a single cell that |
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20:46 | and divides after several hours. So cells are present that it becomes visible |
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20:50 | the naked eye. So the colony , you don't consider a microbe. |
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20:54 | biofilm is not considered micro but of the entities making those each up would |
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20:59 | a microbe. Okay, so again there's gonna be some of these um |
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21:05 | on on the microbe definition. so I'm sure you know, you |
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21:10 | obviously requires a microscope to be observed you're defining microbe typically uh sailor entities |
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21:17 | there's an asterisk because viruses are not . Okay but we do consider those |
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21:22 | . Uh They're not multicellular types. not multicellular animals in time. And |
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21:28 | cells, cellular types of microbes, of course have features that other cells |
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21:33 | , but they typically live independently. can have arrangements. So especially for |
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21:40 | and archaea. Uh they can have changed. It can be clusters, |
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21:45 | can be filament, so it expands morphology. Okay. Um and so |
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21:53 | wise, you see the size of here. So it'd be good to |
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21:57 | kind of the average range of each . Right? Your eukaryotes and prokaryotes |
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22:01 | viruses. Okay, so 20 and is simply your eukaryotic cells and |
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22:09 | 1 to 10 microns. Or procure less than one micron virus is the |
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22:15 | limit is around .2 microns. Uh that I think believe rabies virus |
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22:25 | is on that lower in the tobacco virus. But regardless there is, |
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22:29 | is a very tiny viruses. Typically need to have a electron microscope. |
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22:37 | . Okay. Um of course there's be some a little bit of |
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22:41 | There can be eukaryotic microbes that may a little under 20 microbes. Some |
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22:45 | carrots can get bigger. Uh so there's a little bit of variation between |
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22:50 | trees. Kind of basically average we see. Okay, in terms |
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22:53 | a lower limit on size. So here you see a flu |
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22:57 | So the lower limit is gonna be in um around here for virus. |
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23:04 | , that's around 20 mike nanometers. so you begin to run into turn |
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23:09 | the fact that um the size of molecules themselves can be a limitation. |
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23:14 | you can only get to us so of a small size. Okay. |
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23:19 | and and it won't work. So that's why viruses really are comprised |
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23:23 | a lot. Because there's not enough to accommodate having a lot of structures |
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23:27 | sign it. Okay, They're basically a protein sack surrounding a genome. |
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23:32 | ? There are some variations. But small size means that they can't really |
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23:37 | a lot of stuff in there, that's not what viruses are about. |
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23:41 | . So if we go um to upper limit and we'll talk about that |
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23:45 | a in a second here. The limit, Right, There are factors |
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23:50 | limit how big a cell can get well. Okay, um and I'll |
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23:56 | that shortly. So who are the ? Well, we can divide it |
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24:01 | sailor and a sailor. Okay. so cellular based life. So your |
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24:07 | and pro Teesta, which would be like eastern molds for fungi. Pro |
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24:12 | algae, protozoa wins and the bacteria archaea. So this differentiates between prokaryotes |
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24:20 | eukaryotes. Right, So fungi, are eukaryotic microbes, eukaryotic micro |
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24:26 | Uh so I'm sure you're aware of archaea and bacteria I'm sure you're familiar |
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24:34 | the basic differences between these two Uh pro carry oats. Of |
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24:40 | the hallmark. There is lacking the state, like organelles. Typically uh |
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24:44 | circuit of chromosome etcetera. Okay, . Archaea the members of that |
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24:51 | And that's the other thing that there's groups of pro cario. There's the |
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24:55 | and the archaea. Um Archaea often extremophiles although they can find them at |
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25:01 | temperatures, right? We actually have of archaea in our bodies, but |
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25:06 | can be found also in extreme environments extremes of temperature and other physical |
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25:12 | Um So you carry out uh as know, this nucleus multiple linear chromosomes |
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25:21 | can reproduce either sexually or a sexually on the type. So, you |
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25:26 | features I'm sure you're already aware of the a cellular side. In terms |
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25:30 | microbes, we have viruses, viruses prions. Okay, so viruses comprised |
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25:35 | protein nucleic acids. Uh Vai roids prions are unique in that one. |
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25:44 | viral loads are basically infectious RNA viruses typically only uh an issue for plants |
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25:51 | is today, there is no known infected by virus roids or anything other |
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25:55 | plants. Certain types, we'll talk that later. But crayons, there |
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26:01 | your familiarity is like the mad cow . That's a prion disease. It's |
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26:05 | infectious protein. Right? So for and prions, it's RNA, viral |
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26:11 | prions and that's the only structures associated it. Okay. Nothing else. |
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26:17 | very unique. Um Okay, so just a word on archaea that uh |
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26:27 | can be grouped into three different loosely grouped into. So if you |
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26:34 | anarchy a typically fits one of these categories while or halo file. |
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26:43 | And some of the characteristics of these thermal files. And you know with |
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26:47 | Kia it's it's very common to in vicinity find bacteria as well. |
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26:53 | So don't think that archaea live by . They are certainly uh in uh |
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27:00 | by side with bacteria because bacteria can thermal files as well. It's just |
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27:04 | archaea tend to be on the upper of these extremes. So for |
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27:08 | hyper thermal files. Right? So what we call upper levels of temperature |
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27:14 | our for these archaea are in the and 10 range hypothermia files we call |
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27:20 | that are 80 degrees and above. , I'm showing here Um bacterial thermal |
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27:27 | are typically in like the 450-70 There can be some differences but don't |
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27:33 | too hung up on that. Uh can be of course aerobic anaerobic |
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27:38 | different types of sulfur metabolize ear's are this group. Again, we'll mention |
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27:44 | things later in the semester. Um jen's. So whereas you can have |
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27:49 | bacteria and archaea thermal files only Archaea are method Mogens. Okay. And |
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27:55 | of course that's the production of methane is a greenhouse gas. Um It's |
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27:59 | anaerobic process. It's very sensitive to . Um found in cows are probably |
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28:08 | number one source of methane and of it's the the archaea method genic archaea |
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28:15 | are in them that produce it. You can't you can't have some combinations |
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28:20 | these features. So you can have pathogens can be thermal files. So |
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28:24 | can it's not unusual to have combinations these features. Um And of course |
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28:30 | also find tangents and in landfills uh treatment plants as well. Uh So |
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28:40 | we'll mention methodologies later in the Halo files of course are salt |
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28:45 | Right? So they go in extreme conditions. Uh These are conditions you |
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28:50 | like say there's some natural bodies of . They're very salty, like the |
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28:54 | sea and great salt lake. Uh are come from manufacturers of sodium |
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29:01 | So they'll take seawater, put them these shallow pools, water evaporates. |
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29:05 | you have a very uh concentrated salt . And that's where these bacteria can |
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29:11 | grow in. Um They do have unusual photos and photosynthetic type. They're |
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29:16 | chlorophyll based. So your familiarity is with plants and algae that photosynthesize. |
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29:22 | you have oxygen and using chlorophyll as pigment. Uh These are very |
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29:28 | They're actually the light absorbing pigments are analogous to retinal. That's in our |
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29:35 | . So very unusual, but a primitive thought to be very predating chlorophyll |
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29:41 | photosynthesis. Um Anyway and so like said, we'll touch on on these |
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29:47 | in the semester, but just to you an idea of what the archaea |
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29:51 | about. Uh viruses as mentioned. of course these are a sailor. |
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29:57 | require a host. And so the is always, are they alive or |
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30:00 | ? Right. And so viruses you don't know you have a viral, |
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30:05 | affected by the virus until you show of some type of disease. |
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30:09 | Um viruses can reside outside of a . And that brings up the question |
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30:14 | in that state, are they alive dead? Because they're not reproducing but |
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30:19 | they may still be viable and by . I mean you can have a |
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30:23 | hanging out on a door knob for . And it's not replicating of course |
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30:28 | the kind of state is that in it could be dead, so to |
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30:32 | . So what that would mean is no longer infectious? It can't even |
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30:35 | a host were around, it wouldn't able to infect because it's no longer |
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30:39 | . But it could just be kind viable in that you touch a door |
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30:44 | and you infect yourself. And it then find its host and begin replicating |
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30:49 | that cell. So the viability of outside their host varies depending on the |
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30:54 | type, environmental conditions etcetera. So I think it's been documented that |
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31:00 | can last can remain viable outside the for days if not a couple of |
|
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31:06 | . So uh so it just depends time. But again the hallmark with |
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31:10 | is they they because they're small and don't carry a lot of material with |
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31:15 | . They rely on a host for like protein synthesis, replication of the |
|
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31:21 | etcetera. Okay, so again, expand on viruses later on. Um |
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31:28 | what we call a sailor type of variations on the microbe concept. |
|
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31:35 | so um the uh so this thing this as kind of uh maybe outliers |
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31:51 | maybe, you know, features that not necessarily outliers. But you |
|
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31:54 | there's there's there's always in biology, everything, not everything always fits in |
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31:59 | nice neat box. Right? There's lots of gray areas where you have |
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32:03 | that don't exactly fit the the So um it's just something you |
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32:10 | Right? And so many times maybe forms or something. But you |
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32:15 | there are there are variations of the concept definition. So super sized cells |
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|
32:21 | one of those. So there's this called margarita magnificat to in fact that |
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32:27 | , this genius style margarita is one contains these very large bacterial types. |
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32:33 | all similar that they have a they sulfur as an energy source. |
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32:39 | But they come in different forms. all of them tend to be kind |
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32:42 | a large size so large. You see them with the naked eye. |
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32:46 | millimeters is something that's the centimeters. you can see that with your naked |
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|
32:49 | . You see the filament over there the right is one of those uh |
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32:53 | certain algal species that can be certain fungal species uh here's a bubble |
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32:59 | . You see there that's quite It's often called sea grapes is another |
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33:05 | , but they are um that's a cell and they're unusual and that that |
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33:11 | cell is actually made up of multiple is what we call multi nuclear. |
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33:15 | we've actually popped. That bubble nuclei go flying. They'll colonize them growing |
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33:20 | another bubble. So it's actually a to spread them if they're if they're |
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33:23 | popped. Okay. Um the microbial so visible to the naked eye. |
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33:31 | we mentioned this in the question So you can have um uh biofilms |
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33:38 | are a an aggregation, a proliferation millions of cells. Okay, biofilm |
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|
33:46 | . We'll talk about that as well in the semester. This it's a |
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|
33:49 | specific phenomenon. Uh It's a gene phenomenon. It's just not it's not |
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33:54 | random just coming together cells. It's it's an orchestrated process, but biofilms |
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34:00 | all about surface. So biofilms begin a surface and then can get so |
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34:05 | that they not only grow two dimensionally the surface but three dimensionally off the |
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34:10 | . And so you see that plugged pipe there representing a tremendous amount of |
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34:15 | growth. So you can find biofilms water pipes uh different types of |
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34:20 | Um So while that massive growth means can see with the naked eye of |
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34:27 | to see the individual microbes, you to have a microscope. So, |
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34:30 | know, microbes can come together to a structure visible to the naked eye |
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34:35 | similarly with a colony on a Okay, then we mentioned already micro |
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34:40 | are multicellular animals. We don't consider microbes. Okay, so kind of |
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34:44 | to this, we talked about the end um the lower end limit on |
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34:51 | , you know, that the size molecules themselves can limit how small an |
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34:55 | can be a cell can be. here's kind of the other spectrum. |
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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 |
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|
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 |
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35:30 | down, that makes it harder to to be able to fulfill the requirements |
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|
35:34 | the self to get enough material in out. Okay. And so as |
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|
35:39 | , diffusion can be an issue. , molecules uh in a in a |
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|
35:45 | said, is all uh need to able to travel right to get to |
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35:49 | if it's a substrate to get their enzyme. So to um so as |
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35:55 | it still gets larger, that can a problem, you carry out to |
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35:58 | around that by by compartmentalizing specific molecules to transport them transport vesicles through a |
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36:09 | through the cytoplasm that there's always you do this because their large size but |
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36:15 | don't have those properties. So uh without a margarita, you see |
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|
36:20 | here's a cross section of one of of its filament structure, right? |
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|
36:25 | so big, right? It's filled nitrate. It's what it does |
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|
36:29 | It has nitrate and it has sulfur here, right? The yellow |
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|
36:35 | And so it actually uses sulfur Like H. Two S. |
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|
36:39 | Or S. O. Could be sulfur. And it can use those |
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|
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 |
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|
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 |
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|
37:03 | mitochondria, right? You use things glucose. Right? And you use |
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|
37:08 | to breathe. And then the as result you produce lots of a |
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|
37:12 | They so they do a little They use hydrogen sulfide or other types |
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37:16 | sulfur compounds oxidize those and then uh reduce nitrite to nitrate nitrate to |
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|
37:25 | And they can produce their energy that in the form of A. |
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|
37:28 | P. S. Okay. So so having a large section of their |
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37:34 | body filled with nitrate gives them a they store sulfur and nitrate this way |
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37:40 | that if they're if they're food limited have a source of energy with them |
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|
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. |
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38:02 | they compartmentalize that in these structures all the cell body length so it can |
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38:10 | the needs of that single cell. it's waiting around that diffusion issue by |
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38:15 | what it needs in different locations So it's it's again it's just you |
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|
38:19 | need I'm not gonna test you on margarita but just the example to show |
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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 |
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38:45 | and have you most you're gonna be the what you call quote normal size |
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|
38:49 | . But you are gonna have some are gonna be in these areas where |
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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 |
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|
39:07 | of course you with all life. like to classify it classify life. |
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|
39:14 | . And uh with microbes of course been done with in variety of ways |
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|
39:27 | the biochemical tests. So you basically anything is about. Okay, what |
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|
39:34 | the similarities and differences? Okay. in history taxonomy that's taken on different |
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|
39:40 | . Right. Initially all you can do is look at the observable features |
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39:45 | you know there's more features in common not then they're more closely related, |
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39:49 | them together. Then if there's not many similarities that later went on to |
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39:56 | with microbes at least a was to a microscope to see them and then |
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40:02 | that there are different types of shapes sizes of microbes. Then later on |
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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 |
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40:18 | Uh then along came of course uh discovery of D. N. |
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|
40:23 | And the ability to isolate D. . A. And look at the |
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|
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 |
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40:44 | how many of these how many of are similar in the same position. |
|
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40:48 | gives you an idea of how related not related they are. Okay, |
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40:53 | you can't use the species definition as done with you carry outs, |
|
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40:58 | Because it relies on sexual reproduction. , uh members are members of a |
|
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41:04 | are part of the same species if only breed within that group, |
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41:08 | doesn't fit with microbes. So we to use these other um, ways |
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|
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 |
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|
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 |
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|
41:54 | animal. But strangely enough, what now know is fungi or actually were |
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42:00 | in the kingdom. Plant type likely they have. If you look at |
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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 |
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|
42:17 | heckle uh late 18 hundreds, 18 and uh takes all the microbes out |
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|
42:29 | the animal plant kingdom and put them a kingdom called pro Teesta. And |
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|
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 |
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|
42:52 | if they really lack any kind of structure. So as we look at |
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|
42:56 | if you look at a a cell he saw that there's really no discernible |
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|
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 |
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55:22 | of microbial ecology you can um take samples and see what's actually out |
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55:28 | What's what are the micro regions that coexisting together what's their metabolic functions and |
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55:34 | are they doing? So this this is very powerful allows you to do |
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55:38 | all without having to try to culture again, you're not gonna from the |
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55:45 | you take, you're only gonna be the culture a very tiny fraction of |
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55:48 | in there. So this allows you expand and really find out what's actually |
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55:53 | there. Okay, it's a very tool. And so um so we |
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55:59 | of segue then a little bit into in human history. So certainly uh |
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56:06 | a historical perspective, my chronology begins they when they become discovered. But |
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56:11 | course before then unknowingly basically we've used for certainly for food production, beer |
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56:19 | wine productions were going on for Okay. And obviously unknowingly as |
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56:25 | they've caused infectious diseases that have decimated population, the world's population at various |
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56:30 | whether the plague, smallpox etcetera. . So discover, of course as |
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56:38 | you've heard through this discussion, you , we've used them for all kinds |
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56:41 | things. Um the benefit, you , for our benefit and for basic |
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56:47 | etcetera. Okay, so when we at um uh discovery of microbes, |
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57:01 | , these two individuals hook and then one hook. Okay. And |
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57:10 | There is Hook produced the first microscope was one that was very low |
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57:17 | So when he actually viewed weren't what he viewed were uh either whole |
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57:23 | uh tissues. Um macroscopic organisms basically he was look at them and see |
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57:32 | they're comprised of. He was actually first person to coin the term |
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57:36 | Okay. But he again he wasn't really at microbes, his Van labor |
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57:42 | a hook that was able to produce microscope. And that's although very odd |
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57:49 | . That is a microscope with a that was able to produce around 300 |
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57:55 | . Magnification. Which is quite remarkable the time. And certainly that will |
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57:59 | you to see very tiny entities such bacteria which you see in the drawings |
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58:04 | . So he's kind of credited with the and he called him animal |
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58:08 | but being kind of the father of for that reason. So um and |
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58:13 | course the discovery of microbes opened up invisible world that hadn't been seen |
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58:19 | Okay. And so uh this this of spontaneous generation, right? A |
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58:28 | life from non life okay, have an idea that's been around for centuries |
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58:33 | . And microbes kind of come into microbes kind of then gives more fuel |
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58:41 | the people that believed in spontaneous generation terms of that they thought microbes could |
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58:47 | from non life. Because before that of course thought all life could this |
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58:52 | happen with. But ready was kind the one to show that okay, |
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58:59 | life, more complex forms of this couldn't happen. And this experiment |
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59:03 | of essentially refuted that so you have remember that during this time, you |
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59:07 | , we're talking all kinds of crazy were around this time, um that |
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59:13 | could, you know, if you an open grain, open grain |
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59:18 | you rats running around. And so idea was, okay, grain grain |
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59:23 | to rats. Uh so all kinds crazy beliefs like this. And |
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59:29 | uh you see a meat carcass hanging a butcher shop, right? And |
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59:32 | see flies around, there's no refrigeration then. So you see flies hovering |
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59:37 | , and then all of a sudden see maggots appear in the meat. |
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59:39 | the maggots are spontaneously arising from the meat. No, not true. |
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59:45 | already really, this proved that by , you know, here's the first |
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59:49 | . And we see flies completely open . Of course flies are able to |
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59:55 | in. And you see maggots appear if you have a cork sealed |
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59:59 | nothing can get in the meat does produce maggots. And then so the |
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60:04 | here was the people that believe in generation. They they're thing was that |
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60:11 | most matter can can produce life, you must have air present, |
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60:18 | What they call the vital force. has to be present. Okay, |
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60:22 | that's the reason for having this flask . Gauze allows air to come |
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60:28 | So they fulfill the criteria that air allowed to be present, but still |
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60:33 | wouldn't form because flies weren't allowed to . So it's the flies laying the |
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60:37 | that give rise to the maggots, not spontaneous generation. And so then |
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60:43 | kind of most people dancing. Say, okay, well, |
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60:47 | spontaneous generation can occur cannot occur with organisms. But describe your microbes as |
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60:53 | said, give them more fuel and , okay, well, it can |
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60:56 | with microbes because if you have a and you leave it open and all |
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61:01 | a sudden cells appear in it. ? And so you see the spellings |
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61:04 | experiment here where ross and again, just like a nutrient broth, growth |
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61:11 | that sustain themselves, that if you it sterilize it, let it cool |
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61:16 | you kept it open, more than would occur. And that's that was |
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61:21 | them that was proof of spontaneous But then if you heated it and |
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61:25 | sealed the flask, well then no occurred. Okay, but again, |
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61:30 | kind of back to this argument up , Right? You have to have |
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61:34 | in there. So the spontaneous the that were pro spontaneous generation said, |
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61:39 | , that that doesn't work because you're allowing air to get in. |
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61:43 | that's why I'm not getting growth air have spontaneous generation. So that current |
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61:48 | not enough to convince anybody that spontaneous wasn't a thing to allow microbes to |
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61:53 | . Okay, so this is then when uh passenger comes in. |
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61:58 | that's actually where I stopped on uh . So that's where we'll pick it |
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62:05 | and we'll get into um uh finishing past your medical microbiology and a little |
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62:12 | about ecology. Okay, so that's , folks. I'll and I'll post |
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62:17 | lecture, so we will see you time. The next one of these |
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62:20 | be live, so I'm not gonna not to turn the recorder on. |
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62:24 | , thanks, folks, |
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