Genome Variability

in this video, we're going to begin our lesson on genome variability. And so scientists have discovered over the years that different strains of a single species can have some genome variability or in other words, different strains of a single species can have some differences in their genome or some differences in their DNA sequences. Now, in order to better understand this genome variability, we need to introduce these two terms that you see down below. And so the genome of all strains within a species is composed of two elements. The first element is called the pan genome and the second element is called the conserved genome or in other words, the core genome. Now the pan genome is referring to all of the genes in every strain of the species. And so this is going to refer to the genes that are unique across different strains as well as the genes that are going to be consistent across different strains. Once again, the pan genome refers to all of the genes in every strain of a species. Now on the other hand, the conserved genome or the core genome does not refer to all of the genes. Instead, it only refers to the genes that are going to be conserved or shared or consistent across every strain of that species. And so in order to better understand these two terms, we have this image that's down below and this image represents the pan genome of uh of a specific species that has three different strains. Strain # one is represented by this green circle, Strain number two is represented by this blue circle over here And then strain # three is represented by this pink circle down below. And so what you'll notice is that these are three different strains of the same species. And when we're collectively looking at all of the genes in every strain of the species, we're looking at the pan genome. And so uh this here represents the pan genome. Uh the genes of strain one strain to and strain three. Now the core genome, the conservative the core genome is only referring to the one the genes that are conserved or shared or consistent. And so in this image, the core genome is represented right here within this shaded area because there's overlap between all three strains. And so we can go ahead and label this as the conserved jeans otherwise known as the core genome. And what we'll see is that the conserved genome is always going to be consistent across uh every strain of that species. But of course each strain is going to have their unique genes as well. And so this year concludes our brief introduction to genome variability. And as we move forward in our course, we're going to talk about some of the elements that contribute to genome variability. So, I'll see you all in our next video

in this video we're going to introduce our mobile genetic elements map. And so the variability between genomes of different strains of the same species is significantly attributed to what scientists call mobile genetic elements. Now, mobile genetic elements are sometimes abbreviated as M G E s for short. And so these mobile genetic elements or MGs are really just segments of DNA that can move as is implied by the term mobile, which means move. And so these are segments of DNA that can move from one DNA molecule to another. And so some examples of mobile genetic elements include plasmids, transpose sins, genomic islands and fage D. N. A. And moving forward in our course, we're going to talk about briefly about each of these different mobile genetic elements in their own individual videos. And so what you'll notice is down below, we're showing you our map of the lesson on mobile genetic elements or MGs. And uh which you'll notice is on the far left. Over here we're going to talk about plasma. It's then here we're going to introduce what are known as trans Pozen's. Then over here we're going to introduce what are called genomic islands. And then last but not least on the far far right, we're going to revisit fage is and fage DNA. And so this does represent a map of our lesson. And so you can use it to help guide you as we move forward in our course. And as always we're gonna be covering the map by following the left most branch first and then zooming out and covering each of these topics as you see in that particular order. And so I'll see you all in our next lesson video to talk more about plasmas.

in this video, we're going to focus on plasmas. And so plasmids can be defined as circular double stranded DNA molecules with an origin of replication, allowing them to replicate within a cell. Now some plasmas are known as high copy number plasmas and these are plasmids that will replicate very fast or very quickly inside of a cell. And other plasmids are known as low copy number plasmids. And so they replicate very very slowly within the cell. Now these high copy number of plasmas that replicate quickly, of course they are going to be found in high numbers or high copy number because they replicate so fast. Whereas the low copy number of plasmas that replicate slowly are going to be found in relatively low numbers within the cell or low copy number. Now these plasmas, regardless if they are high copy number or low copy number. Plasmas can carry various genes and sometimes some of those genes are going to be able to provide the cell with the ability to survive um in a particular environment, such as an environment that contains antibiotics for example. And so we call these plasmas resistance plasmas, otherwise known as our plasmas. And so resistance plasmids or are plasmas are plasmas that encode genes that confer resistance to antibiotics, allowing the cell to survive in the presence of antibiotics. And these genes that are found on the resistance plasmas are sometimes referred to as our genes. Now in addition to the our genes, it's important to note that these plasmas can also have other genes and uh the resistance plasmids, most of them are going to be conjugated plasmas, which means that these plasmids can be horizontally transferred between different species via conjugation. And once again outside of the our genes, they can also contain other genes that are required for DNA transfer by conjugation. And so if we take a look at our image down below, over here, on the left hand side, notice that the top half of this image is focusing in on high copy number plasmas and high copy number of plasmas which will notice as they replicate very very quickly within the cell. And so they're going to be found in relatively high numbers, high copy numbers within the cell. Whereas the low copy number of plasmas on the bottom half over here notice that they replicate very very slowly over time. And so they're going to be found in relatively low numbers within the cell. Now, over here is a representation of a plasma and some of the different regions of DNA that can be found within the plasma. And so what you'll notice is that it contains an origin of replication allowing it to replicate and this is specifically and our plasma here a resistance plasma um and uh it's a resistance plastic because it contains specific genes that allow for antibiotic resistance such as an amp. Our gene which allows for ampicillin resistance, a gene that allows for ample cylinder resistance, allowing the cell to survive in the presence of ampicillin up at the top is a region a gene, the tet are gene or for tetracycline resistance resistance to yet another antibiotic. And then over here in purple. What we have is a can R. Jean providing resistance to an antibiotic called can um Iceland. And also in addition to being our plasma. It's also a conjugated plasma as well because it contains this tribal region or T. R. A. Region here which is the region that is important for conjugation, allowing the our plasma to be uh horizontally transferred and passed from cell to cell via conjugation. And that also allows for the spreading of resistance genes. As you see here between different uh species of bacteria. And so this year uh concludes our brief lesson on plasmids and how they contribute to genome variability because they are mobile genetic elements that can be passed from uh one cell to another cell via congregation. And so we'll be able to talk about other mobile genetic elements as we move forward in our course. So I'll see you all in our next video

in this video we're going to introduce transpose sins. And so transpose sins are also sometimes referred to as jumping genes. And so transpose sins or jumping genes are really just referring to pieces of DNA that have the ability to alter or change their locations within the cell's genome. And transpose sins are able to alter their locations within the cell's genome through a process known as trans position. And so trans position is really just the name of the process that allows transpose sins to alter their locations within a cell's genome. And so transposition is really just the process of the movement of a transpose on to a different location within the cell's genome now transpose ons themselves because they are pieces of DNA. They do encode uh for a protein, specifically an enzyme. They encode for an enzyme known as transposes. And so anything that ends in A. S. E. Is an indication that it is an enzyme. And so transposes is an enzyme that is going to catalyze transposition, allowing the transposed on to move to different locations within the cell's genome. Now sometimes transposition can lead to what is known as insertion allele in activation. And so insertion tool inactivation is when the gene that a transpose on jumps into or gets inserted into becomes inactivated. And so we can get a better understanding of transpose sins. Transposition and insertion elin activation as we look at our image down below And so notice that this is an image of transpose isn't or jumping genes. And so notice on the left hand side over here we're showing you a bacterial cell and you can see in blue it represents the bacterial chromosome. And which will notice is that the little green region that you see over here on the left of the chromosome, this is referring to the transpose. Um and then over on the left you have the little yellow region of the chromosome and this is referring to jean X. Just another gene within the cell. And so zooming into just this specific region. Uh that is what this part is doing over here and again the transpose on is capable of transposition, meaning that it can change its location within the cell's genome. And so notice that the starting position once again is over on the left hand side of the chromosome. However the transpose on also known as a jumping gene can change its location and insert itself into a different region within the chromosome. And so just like this frog here can jump into a different location. This gene this transpose on can jump into a different region. And so gene X which will notice is as it is here in this image, GENE X is active. However, after transposition occurs after the movement of the transposition occurs uh it could possibly lead to insertion all an activation. And this is when the transpose on inserts itself into a gene to inactivated. And so the transpose on ending position which will notice is over here on the right is it is inserted into gene X. And therefore it disrupts and in activates gene X. And so um what you can see is that transpose ions can help to create genetic variability and in cases some cases it can lead to insertion inactivation to inactivate specific genes. And so this year concludes our brief lesson on transpose sins, transposition and insertion elin activation. And we'll be able to get some practice applying these concepts and learn about other mobile genetic elements as we move forward in our course. So I'll see you all in our next video.

in this video, we're going to briefly introduce genomic islands. And so genomic islands are really just referring to relatively large regions of the bacteria's chromosome that is actually believed to have originated in a different species. And so this bacteria would have obtained the genomic island through some form of horizontal gene transfer. Now these genomic islands can be identified by scientists because the genomic islands have a unique ratio of G. C. Base pairs. And recall that Gs and CS are referring to the nitrogenous bases or the sequence of the DNA. And so these G. C base pairs have unique ratios within different species. And so the genomic island will have a unique G. C ratio that is different than the rest of the cells chromosome and the rest of the cells chromosome has a different G. C ratio. Now pathogenesis, the islands are specific types of genomic islands that contain genes giving the sell the ability to cause disease. And so anything that is a pathogen is uh an agent that is capable of causing disease. And so if we take a look at our image down below, notice that this is showing you a bacterial cell and within the bacterial cell you have the bacterial cells genome its chromosome here. And what you'll notice is that this chromosome is colored into two different regions. It has this relatively large region here which is going to be the genomic island. Specifically. This is going to be a path oh genesis city Island a specific type of genomic island that makes the cell pathogenic allowing it to cause disease. And what you'll notice is that the pathogenesis the island is going to have a specific ratio of G. C. Base pairs. That differs from the G. C. Ratio of the rest of the cells chromosomes. And so this pathogenesis the island does somewhat seems like a little island here in the middle of an ocean if you will. And so that this is somewhat why you can see why they might be called genomic islands because they some what appeared to be like a little island here uh that is surrounded by uh DNA sequences that have different G. C ratios. And so this here concludes our brief introduction to genomic islands. And we'll be able to get a little bit of practice on these concepts as we move forward and then talk about fage is as the last mobile genetic elements. So I'll see you all there.

in this video we're going to talk about fage D. N. A. As a mobile genetic element. And so first we need to recall from our previous lesson videos that fe ages or bacteria pages are particles of DNA. Or RNA surrounded by a protein coat. And really these fage is serve as viruses that infect bacteria. And also recall from our previous lesson videos that certain types of pages are capable of inserting their DNA into the host cells chromosome creating what scientists call a pro fage. And so the pro fage can be replicated along with the remainder of the chromosome and therefore the pro fage can be passed on to the progeny of the cells or to the offspring of the cells. And so fage D. N. A. Is a mobile genetic element because it's capable of moving and being transferred to different organisms. And so what you'll see here in this image is a fage infecting a bacterial cell and injecting its genetic material, injecting the fage D. N. A. And then the phase D. N. A. Can of course integrate into the host cells chromosome to create a profile page as we see over here and then once the pro fage the viral DNA here is integrated. It can then be replicated and passed down as this cell replicates and divides. And so this is a mobile genetic element that can essentially be transferred between different organisms and passed down. And so this here concludes our brief lesson on fage D. N. A. As a mobile genetic elements. And we'll be able to get some practice applying these concepts as we move forward, so I'll see you all in our next video.