mosquito genome

A general method and good student project for finding interesting anomalies in GenBank

sporte — Thu, 25 Sep 2008 06:21:34 +0000

A general method and good student project for finding interesting anomalies in GenBank

Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank

This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things.

In this last part, I discuss a general method for finding novel things in GenBank and how this kind of project could be a good sort of discovery, inquiry-based project for biology, microbiology, or bioinformatics students.

I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank

A general method for finding interesting things in GenBank

*Note: I'm including the first two steps for reference. If you like, you can go straight to the links in step 3 and find the viruses. If you want to see how this method works, take a look at the other parts in this series and see how I found a gene from a paramxyovirus in a mosquito genome

1. We begin by going to the NCBI.

2. Use either one of these two paths to get to the Entrez Genomes Home page.

Select Genome from the pull-down menu on the home page and click the Go button.
Click the Go button on the home page and click the link to the Genome database.

3. Look on the left side of the page for Viruses. Click either Viruses, Phage, or Viroids.

Viruses: takes you to a list of at least 2652 genome sequences for viruses that infect eucaryotes.
Phage, you go to a list of at least 500 viruses that infect bacteria.
Viroids - you'll a list of 39 viroid sequences.

I suggest using viruses, phage, or viroids because their genomes are small, they generally match other viral sequences best, and it's not too daunting to look at less than 10 proteins in sufficient detail.

4. Select the Accession number link to get to the genome sequence. Note - some viruses, like influenza, have genomes that consist of physically separate pieces. For those viruses, you may need to look at each piece.

5. You should now be at a page with a table that contains information about the viral genome. Scroll to the very bottom of the page and look for the link to the Sequence Viewer and click it.

6. Mouse over the red bars that represent protein sequences and use Blink to examine the blast results for each protein in the genome, one by one, just as I did here.

The cool thing about Blink is that shows the blast results grouped by the type of organism. This is very helpful for finding needles in haystacks.

7. Examine the Blink results and investigate any matches that are not viruses. Some of these matches will actually be to viral proteins that are in the wrong database, some will be to undiscovered viruses, and some, well, who knows what we'll find.

Have fun!

sporte Thu, 09/25/2008 - 02:21

Do mosquitoes get the mumps?, part IV

sporte — Wed, 24 Sep 2008 06:43:03 +0000

Do mosquitoes get the mumps?, part IV

Part IV. Assembling the details and making the case for a novel paramyxovirus

This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.

image from the Public Health Library

I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a novel mosquito paramyxovirus
V. A general method for finding interesting things in GenBank

In part III, I wrote about using Blink to find matches to the mumps RNA-dependent RNA polymerase (also known as a "replicase") and the surprise of finding a really good match in the genome from Aedes aegypti (a type of mosquito that carries yellow fever and dengue virus).

The curious thing about this match is that no other metazoan genome contains a match to this viral protein. This makes sense. Metazoans, like us, other animals and insects, don't need to make copies of RNA sequences, especially not RNA molecules that are hanging out in the cytoplasm. The only guys who need an enzyme like this are viruses.

I can think of three possible explanations for why we might seeing this gene in the Aedes aegypti genome.

Case A. There's a mistake in the genome assembly.

Case B. The replicase gene really is a normal part of the mosquito genome and somehow got missed in the blast search.

Case C. The replicase gene ended up in the Aedes aegypti genome through the actions of a retrotransposon, and the presence of this sequence might be unique to the strain of mosquitoes used for the genome sequence.

There could be more explanations but these are all I can think of right now. Let's go through each case and see how the evidence supports or refutes each one.

Case A. There's a mistake in the genome assembly.

When I first found the replicase gene in the mosquito genome, I was pretty sure that this was a mistake in the sequence assembly. There are quite a few repetitive sequences in the Aedes aegypti genome that surrond the replicase gene. Those kinds of sequences are notorious for causing mistakes in assemblies. And the replicase gene appears to be located in a supercontig whose assembly hasn't yet been completed.

Plus, we know in part II, we found that Li et. al. (1) discovered a new virus in a cell line when they were trying to identify genes turned on by angiotensin.

But, the more I thought about it, the less this explanation made sense. When Li did their work, they were isolating RNA, making DNA copies (cDNA), and sequencing the cDNA. It makes sense in their case that, if there happened to be any RNA viruses in the cell, those would also get converted to cDNA, and would get sequenced along with the human RNA molecules (or in Li's case, the rat RNA molecules).

The mosquito genome was sequenced by scientists at the Broad Institute and published in Science in 2007 (2). In reading the paper, we can see how the sequencing process worked. The Broad scientists made libraries of cloned DNA fragments, sequenced the DNA, then assembled the sequences together. Paramyxoviruses, however, are made from RNA. You can't clone RNA unless you convert it to cDNA first, and that wasn't part of the process. It's sad, but the nice neat explanation falls apart when we review the experiment.

Case B. The replicase gene really is a normal part of the mosquito genome and somehow got missed in the blast search.

To check this, I decided to look at VectorBase VectorBase is a specialized database for researching the genomes of insects that transmit disease. At VectorBase, you can find genome sequences for mosquitoes like Anopheles gambiae, Aedes aegypti, and the house mosquito Culex pipiens; as well Ixodes scapularis (tick), Pediculus humanus (louse), and others. You also find standard tools for comparing and aligning sequences, tools for looking at gene expression and some specialized tools for comparing genomes.

I compared the region of the Aedes aegypti genome that contains the replicase gene with the corresponding regions in two other mosquito genomes, the one from Anopheles gambiae and Culex pipiens. I found from this, and other blast searches, that the replicase gene is not present in those other mosquito genomes.

Case B is ruled out.

Case C. The replicase gene ended up in the Aedes aegypti genome through the actions of a retrotransposon, and the presence of this sequence might be unique to the strain of mosquitoes used for the genome sequence.

Ruling out cases A and B, leave us in the end with case C. Retrotransposons are really cool elements in the genome that are a bit similar to retroviruses. They are found in the nuclear DNA. They can be transcribed into RNA and, here's what's wild about them, they make reverse transcriptases that produce DNA copies of their RNA and then, they also make an integrase that helps them move into new places in the genome.

Why do I think a retrotransposon might be involved?
Galagan et. al. found that the Aedes aegypti genome is chock full of retrotransposons. Plus, there's a sequence from a retrotransposon called "Pao_Bel," overlapping the end of the replicase gene.

I should mention, too, that while Galagan et. al. didn't say anything about this replicase in their 2007 paper, they did mention finding 6 flavivirus sequences incorporated in the genome. Those sequences could have been put in the genome in a similar way.

What's the take home message?

Now it's time to play Hercule Poirot and use those little gray cells to try and reconstruct what happened.

I think an ancestor to the Liverpool mosquito was buzzing around one day and sucked some nectar from a plant and got a snoot full of a plant virus. I don't know much about insect reproduction or how the virus ended up near the newly forming germ line cells, but these viruses can make cells fuse together, so I can imagine this happening somehow. When the mosquito cells were dividing, a retrotransposon copied part of the viral RNA and caused it to get integrated into the host genome.

It would be really interesting to see if other strains of Aedes aegypti share this gene and maybe even use PCR to try and find paramyxoviruses in wild insects.

Tomorrow, I will describe a general technique for finding anomalies and discovering interesting things in GenBank.

References:

Z LI, M YU, H ZHANG, D MAGOFFIN, P JACK, A HYATT, H WANG, L WANG (2006). Beilong virus, a novel paramyxovirus with the largest genome of non-segmented negative-stranded RNA viruses Virology, 346 (1), 219-228 DOI: 10.1016/j.virol.2005.10.039.
V. Nene, J. R. Wortman, D. Lawson, B. Haas, C. Kodira, Z. Tu, B. Loftus, Z. Xi, K. Megy, M. Grabherr, Q. Ren, E. M. Zdobnov, N. F. Lobo, K. S. Campbell, S. E. Brown, M. F. Bonaldo, J. Zhu, S. P. Sinkins, D. G. Hogenkamp, P. Amedeo, P. Arensburger, P. W. Atkinson, S. Bidwell, J. Biedler, E. Birney, R. V. Bruggner, J. Costas, M. R. Coy, J. Crabtree, M. Crawford, B. deBruyn, D. DeCaprio, K. Eiglmeier, E. Eisenstadt, H. El-Dorry, W. M. Gelbart, S. L. Gomes, M. Hammond, L. I. Hannick, J. R. Hogan, M. H. Holmes, D. Jaffe, J. S. Johnston, R. C. Kennedy, H. Koo, S. Kravitz, E. V. Kriventseva, D. Kulp, K. LaButti, E. Lee, S. Li, D. D. Lovin, C. Mao, E. Mauceli, C. F. M. Menck, J. R. Miller, P. Montgomery, A. Mori, A. L. Nascimento, H. F. Naveira, C. Nusbaum, S. O'Leary, J. Orvis, M. Pertea, H. Quesneville, K. R. Reidenbach, Y.-H. Rogers, C. W. Roth, J. R. Schneider, M. Schatz, M. Shumway, M. Stanke, E. O. Stinson, J. M. C. Tubio, J. P. VanZee, S. Verjovski-Almeida, D. Werner, O. White, S. Wyder, Q. Zeng, Q. Zhao, Y. Zhao, C. A. Hill, A. S. Raikhel, M. B. Soares, D. L. Knudson, N. H. Lee, J. Galagan, S. L. Salzberg, I. T. Paulsen, G. Dimopoulos, F. H. Collins, B. Birren, C. M. Fraser-Liggett, D. W. Severson (2007). Genome Sequence of Aedes aegypti, a Major Arbovirus Vector Science, 316 (5832), 1718-1723 DOI: 10.1126/science.1138878

sporte Wed, 09/24/2008 - 02:43

Do mosquitoes get the mumps?, part III

sporte — Tue, 23 Sep 2008 08:00:14 +0000

Do mosquitoes get the mumps?, part III

Part III. Serendipity strikes when we Blink

In which we find an unexpected result when we Blink while looking at the mumps polymerase.

This is the third in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes. And yes, this is where the discovery happens.

To paraphrase Louis Pasteur, discovery favors the prepared mind, and yesterday's work was good preparation for today's discovery.

Some of our take home lessons from yesterday were these:

1. Viral proteins usually match viral proteins.
2. If we see matches to non-viral proteins, there may be something interesting going on.

What does the L protein do? Does L stand for Last?
Yesterday, we skipped the very last one of the mumps proteins when we worked our way through the mumps proteome. That protein is the L protein and its job is to copy the mumps genome. Many viruses reproduce by borrowing proteins from their host cell. They use their host's DNA or RNA polymerases to copy their genomes and they use their host's ribosomes to make their proteins.

Mumps can borrow ribosomes but it can't just ask the cell if it can borrow a polymerase. Eucaryotic cells keep their RNA polymerases locked up inside the nucleus where mumps can't get at them. Then, even if mumps could get access to the host's RNA polymerases, the host cell's RNA polymerase won't work. It only copies DNA, not RNA!

Being an occasional adjunct faculty member, this situation reminds me of what it's like when I want to use the department copy machine to copy assignments. I can't always get to the copy machine very easily, since it may be locked up somewhere in a special copy room. Then, when I get a key and find my way to the copy machine, the machine won't work because it needs some kind of special code (analogous to the DNA). I suppose I shouldn't be comparing adjunct faculty to viruses, but what the heck, in this case it kind of works.

The mumps virus has a similar problem. So, rather than try and mess with getting into the nucleus and changing the host's RNA polymerase, mumps makes it's RNA-dependent RNA polymerase.

Well, what happens if we Blink the mumps L protein?

When I select Blink, I see that there are 717 viral proteins that match the mumps L protein and 2 proteins from Metazoans. By now, you may have guessed which ones I'll find interesting.

When I ask Blink to show me the Metazoans, I find that both links are to the same hypothetical protein from Aedes aegypti (a mosquito that can carry yellow fever virus and dengue virus).

The matching region is also pretty long, 853 amino acids. I also see that, lo and behold, there's a link to the Conserved Domain Database. If I follow it, I can see that I'm hitting a conserved domain that's found in the Paramyxovirus RNA dependent RNA polymerase, and with an e-value of 2 x 10^-57. In other words, we can be pretty confident that this hypothetical mosquito protein is very similar to an RNA-dependent RNA polymerase.

But this is weird. Why should a mosquito have an RNA-dependent RNA polymerase?

Mosquitoes don't have any need to copy anti-sense RNA.

How do we know that mosquitoes and other insects don't contain a protein like this and we've missed it?

We can Blink with our mosquito sequence. Blinking will let me see if there are any other mosquito proteins in GenBank that match my replicase sequence.

To do this, I click the little blue diamond to the left of the row and I get a whole new set of Blink results.

These Blink results only showed matches to 559 viral proteins and one metazoan protein (the other record for the same mosquito sequence, you can think about this one as a positive control).

The best matches were to the replicases from a bunch of plant viruses (orchid, maize, rice, strawberry, lettuce, and others). For the Orchid fleck virus, the e value was 1 x 10^-24. In other words, the probability of finding a match this good in a database of random sequences would be 1 over a 1 followed by 24 zeros. Very small.

It was interesting to see that the best matches were to plant viruses. In fact, when I selected the multiple alignment tab from the Blink results and used the NCBI Blink options to build a tree from the best matching 100 viral polymerases, sure enough, the mosquito sequence was still closest to the viruses from plants.

This is interesting because mosquitos pollinate certain kinds of orchids. I don't know if mosquitoes pollinate strawberries, but they definitely pollinate blueberries. So, maybe finding a viral RNA polymerase in a mosquito that's most similar to the Strawberry crinkle virus or Orchid fleck virus makes sense.

The curious thing now, is how did a viral sequence end up getting assembled into the Aedes aegypti genome? Does it belong there?

That's our subject for post IV.

sporte Tue, 09/23/2008 - 04:00

Do mosquitoes get the mumps?, part II

sporte — Mon, 22 Sep 2008 15:00:36 +0000

Do mosquitoes get the mumps?, part II

Part II. What do mumps proteins do? And how do we find out?

This is the second in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes, and a general method for finding interesting things.

In Part I, we looked at the NCBI SeqViewer, and found a new way to check out a genome map, and learn more about individual genes and proteins.

When we look at proteins from the mumps virus what do we find?

To be honest, I was a lot more random about this when I was playing, but once I found something, I realized it would better to be more systematic and look at each protein one by one.

If I go through all the proteins and systematically review them with Blink, for almost all of the proteins, I find the kind of things that I'd expect. I also find the links that will tell me what the proteins do - at least as far as we know.

Wait, wait, wait! What is Blink?

Oh, sorry.

When protein sequences, either confirmed or predicted, enter GenBank, the NCBI has an automated system that uses blastp to compare these sequences to all of the sequences in the protein sequence databases. These results can be accessed by selecting the Blink link.

Why is Blink helpful?
There are many reasons. First, you don't have to wait for blast or do the blast search yourself. Second, you get many more results than you would from a normal blastp search and the results are organized by kingdom. Usually, when you do a blastp search you only about a hundred results, by default, and you don't see everything that's there unless you think to look for it. Third, you can filter the results in interesting ways. For example, if you just want to see protein sequences that are in 3-D structures, you can do that. You can also get multiple alignments and phylogenetic trees from Blink.

Anyway back to our story.

What do we get if we Blink when we're looking at the mumps proteins?

First, I can find something about the function of each of the eight mumps proteins. This will be the focus of today's post.

To use Blink, I found a record for mumps in the NCBI genome database and selected the Sequence Viewer link (see part I for instructions). I liked this method because I could see all the proteins encoded by the mumps genome in one view and look at them one by one.

Here's what this looks like:

I got this menu by holding my mouse over the red protein graph on the far left side of the map. You can see in the yellow menu that this protein is a nucleocapsid protein.

Then, I clicked the Blink link at the bottom of the menu to find out what it does.

Not surprisingly, I found that the nucleocapsid protein only matched proteins from other viruses. The three sequences in the Other category were from constructs. Then I selected the link to the first sequence to see if I could learn more from the protein record. This part involved a bit of trial and error. Some records had information, some did not.

This record told me that the mumps nucleocapsid protein, NP_054707.1, protects the viral RNA genome, along with some other information about the structure of the protein.

The next two proteins are encoded by the same gene: V/P. The V protein is the smaller of the two proteins. And, the P protein shows us that GenBank is missing a spell check function.

The P protein should be listed as a "phosphoprotein" but the name in the menu is "phoshoprotein."

Sigh. When I look at the Blink results, I can see that about half of the matching sequences have the same spelling error. I also see that this sequence matches proteins from 256 viruses and nothing in any other kingdoms.

What does the phosphoprotein do?
Selecting the link to the first sequence, I find some interesting things. First, this protein is made by editing the viral RNA. Ooooh! I love RNA editing. Second, this protein is part of the viral RNA polymerase and it helps make proteins.

The other protein that's encoded by the same gene, the V protein, is made from unedited RNA. This protein matches sequences in 215 viruses and nothing else. And, it's thought to block interferon. Interferons are proteins that help defend us from certain kinds of viruses.

The next protein is M, or membrane protein. Interestingly, this protein matches 468 viruses and one metazoan sequence. This is cool!

Why?

Because we are metazoans. If we click Metazoa, we see which metazoan sequence is matching our mysterious membrane protein.

Our Blink results imply that this sequence is human. But, if we click the accession number for this sequence, we see that this sequence comes from a paper with this intriguing title:

Beilong virus, a novel paramyxovirus with the largest genome of non-segmented negative-stranded RNA viruses

Ah, hah! This wasn't a human sequence at all. Interestingly, the GenBank record states that this sequence came from a Homo sapiens (human) mesengial cell, but when I looked at the abstract for the paper, the abstract says that this virus probably came from a rat mesangial cell line, not a human cell at all. It just goes to show, it's not enough to look at the databases, you do need to read the papers or at least the abstracts.

Anyway, what does the membrane or matrix protein do for the mumps virus? The GenBank record for P33482 says that this protein is involved in assembly of the viral particle, and it interacts with the viral membrane.

Onward.

Next we have the F or fusion protein. This protein matches sequences in 3793 viruses and 3 sequences in metazoans.

Let's check out those metazoan sequences.

The three metazoan sequences are:
1. Angrgm-52 from Homo sapiens

and

2. Two different entries for the same sequence, the original entry EDV20972, and the same sequence as a reference sequence, XP_002116616. Both of these sequences are described as hypothetical sequences from the genome of Trichoplax adhaerens.

What can we say about these results?

First, the supposedly human Angrgrm-52 sequence comes from the same set of sequences of supposedly human mesanglial sequences that contained a paramyxovirus (Li, et. al.). The GenBank record for this sequence, AAL62340, hasn't been updated yet, but I think we can be pretty confident that this a viral sequence and not a human sequence.

Next, I know very little about Trichoplax adhaerens. The genome sequencing proposal says it's a simple multicellular, marine organism lives in tropical waters around the world. The proposal also has lots more information about it if you're interested.

Maybe. When I look at the match, the aligning region is a little on the short side, only 100 of the 538 amino acids are aligning to the hypothetical Trichoplax sequence. A paramyxovirus sequence may have gotten included in the Trichoplax genome assembly, the evidence isn't as strong though, as it was in the rat cell line.

I almost forgot. What does the mumps fusion protein do?

From the GenBank record for P11236, we find that the fusion protein helps the membrane of the virus fuse with the membrane of the cell.

We're almost done.

The next protein is a small hydrophobic protein. It only matches viral proteins and the GenBank record for P22112 says that it probably functions by inhibiting TNF-alpha signaling and block apoptosis (a special kind of cell-death) in infected cells. These functions are inferred from the sequence similarity to other proteins.

Our last protein for today, is the hemagglutinin-neuraminidase. This protein matches 830 viral proteins and it functions by binding to receptors - helping the virus to infect the right kind of cell - and by cutting sugars off of cells - allowing the virus to escape from dead cells.

Wheew! That's enough for today. We'll look at the last protein sequence (the L protein) in part III.

Reference:
Z LI, M YU, H ZHANG, D MAGOFFIN, P JACK, A HYATT, H WANG, L WANG (2006). Beilong virus, a novel paramyxovirus with the largest genome of non-segmented negative-stranded RNA viruses Virology, 346 (1), 219-228 DOI: 10.1016/j.virol.2005.10.039

sporte Mon, 09/22/2008 - 11:00

Question: If human ancestors one million years ago lived along tropical marine seashores and consumed marine shellfish and incidentally the organism Trichoplax adhaerens, could there have been a derived infection of mumps in humans, that was then spread socially via contagious social behavior? Or did I confuse things?

I don't think that's the answer. Mumps belongs to a family of related viruses called the Paramyxoviridae, or paramyxoviruses. These infect birds, dogs, pigs, dolphins, porpoises, whales, humans, chimps, salmon, reptiles, snakes, sheep, cows, and mice.

I think finding sequences that are similar to a mumps protein in Trichoplax adhaerens just says that members of the paramyxovirus family are more widely distributed than we thought. What I've done so far doesn't tell us anything about where the Trichoplax virus came from or who it's closest relatives are in the paramyxo family.

Do mosquitoes get the mumps?, part I

sporte — Sun, 21 Sep 2008 14:03:41 +0000

Do mosquitoes get the mumps?, part I

Part I. The back story from the genome record

Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank.

I began this series on mumps intending to write about immunology and how vaccines work to stimulate the immune system. I still plan to write about vaccines, because I love immunology, but .....well........ along the way, I decided to play a bit with the sequences in the mumps genome. I can't help it. You can learn a lot about a virus from the proteins it makes.

Getting the back-story from the genome record

I did what I usually do when I want to learn about a new virus. I went to the NCBI and searched for the mumps virus genome among the 1600 or so eukaryotic viral genomes that have been sequenced. Finding the genome sequence told me that mumps has a single-stranded genome; 15,384 bases long; made of RNA. Unlike some single stranded RNA viruses like influenza, the mumps genome is in one piece.

Interestingly, mumps RNA can't be translated directly into protein. Mumps RNA is complementary to the RNA strand that would be used for translation. This means that mumps requires an extra step in the decoding process. The mumps RNA has to be copied first in order to produce the complementary copy that gets used to direct production of mumps proteins. This is a lot like transcription, except that the template is RNA instead of DNA.

This business of copying RNA is unusual enough. Copying the RNA also happens in an unusual place. Normally, nucleic acids get copied in a special compartment, the nucleus. In the case of mumps and other single-stranded RNA viruses, all the RNA copying happens outside of the nucleus in the cytoplasm. Mumps, of course, also has to bring it's own enzyme along to do the job, since eucaryotic cells don't normally do this kind of work.

When I followed the taxonomy links, I could also see that other paramyxoviruses, related to mumps, have been found in fish (salmon), snakes, dogs, sheep, and pigs.

On to the research
I went back to the mumps genome record and looked a bit closer.

It was then I noticed it. There was a brand new, itty bitty link below the graph of the genome.

"Click me!" it said.

Feeling a little like Alice in Wonderland, I clicked it, wondering all along if I was going somewhere interesting or falling into a rabbit hole.

The other end of the link

Luckily, it turned out to be interesting.

The green graph (top) shows the positions of the genes, the red graph on the bottom shows proteins. You can see the second gene encodes two different proteins. That's kind of neat. I found, too, that when I held my cursor over the sequences, menus appeared with links to various things that I could do. It turned out I could get FASTA sequences, GenBank records, and pre-computed BLAST results.

Web pages at the NCBI are oddly reminiscent of the games that my kids used to play. My daughters used to spend hours playing Millie's Math House and something with Fribbles. Even today, I can hear them singing along with the theme music to Millie's Math House. And there aren't any words!

Anyway, in Millie's Math House, you had to click objects to find out what they would do. The pages at the NCBI are designed the same way. There's no way of guessing ahead of time, you just have to take the plunge and either move your mouse over things or click on random objects, just in case.

Notice below, I moved my mouse over one of the maps of a protein sequence and I found lots of links.

Next, I started randomly clicking protein sequences and finding out what they matched.

You can do this yourself and jump ahead or wait until tomorrow and see what I found.

sporte Sun, 09/21/2008 - 10:03

Help me out here, do organisms need additional enzymes for each break in their genome if they're copying in the cytoplasm?

I don't think so. Orthomyxoviruses like influenza have genomes that are broken into different segments and I don't think they have special enzymes for dealing with that.

This wouldn't matter for paramyxoviruses like mumps, though. The genome isn't broken into segments, it's all in one piece.