6/7 Hrs of VPg

6/7 hours (another 2/3 hrs in writing this entry) ... searching through net.... lots of research papers... At last, I've figured it out.

Yesterday, SRK was taking her lecture on plus strand RNA virus: Poliovirus and its life cycle.

The genome length of this novel (!!!) virus is 7500 b (According to SRK, but I think it varies. I've seen the range 7440 to 7700 b in different research papers.) Some features of Poliovirus genome are given below:

1. It has a covalently attached protein, VPg, at its 5' end. (¹)
2. Poly (A) tail at 3' end.
3. Three types of genes are present in this monocistronic genome: Structural, Protease (or proteinase) and RNA polymerase (from 5' to 3' respectively.) These genes are translated as single long polyprotein (~247 kD).









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4. The proteinase has autosplicing capability. At first, it splices out itself, then it cleaves the polypeptide into different structural proteins and enzymes.

The list can be made much longer.

SRK said, poly (A) tail is required for infectivity, but VPg isn't. Later she said, RNA strand without covalently attached VPg can't be incorporated into viral capsid in maturation stage. I thought there was something missing... but I preferred not to ask. But this time Shammu was the person. She asked,"How can a RNA virus (or its RNA) be infective when it can't be inserted into viral capsid?" It was a good question, and I think I gave the answer in the class. But SRK didn't get my answer. Actually she didn't get the question either. She checked her lecture sheet and a book she brought with her (most probably Brock's Microbiology), then she dismissed one of her previous words. She thought it was her old book which is responsible. She told, "Forget about the sentence, "RNA with VPg can't be transcribed."...Well, Well, Well... this is another new statement. I don't think she told this before! May be I've missed.

So how to solve the puzzle. Remember none of her statements were wrong.

I've read some research papers published in different journals in between 1977 and 2006. The riddle is nearly solved ;)

VPg acts as a primer for new RNA strand synthesis (for both"+" and "-" strand synthesis.(^2,3)) It also stabilizes the RNA in cellular milieu. Recall cellular mRNAs are stabilized by 5'-cap. So VPg is necessary for replication of viral RNA. The RNA polymerase is coded by viral genome. RNA dependent RNA polymerase (RDR)... this enzyme requires primer, as far as I know other RNA polymerase don't require primer.

So what about translation? Before translation, VPg is cleaved by cellular enzymes. RNAs attached to VPg can't be translated. The reason isn't still known, but it is thought that VPg interferes with some steps in translation. (²) 3D folded structure, Cis-acting Replication Element (cre) which along with Internal Ribosome Entry Site (IRES) plays vital role in initiation of translation... I am not sure whether cre and IRES are the same sequences or two different sequences... I'll update when I know.


Update: cre isn't necessary for translation, rather it is required for replication. cre is located within IRES but mutation in conserved cre region (AAACA motif) doesn't effect the rate of translation. (⁴)



Hurray! The dilemma is solved at last. Polio RNA without VPg is infectious since it can carry out penetration, translation, synthesize new VPg protein which can act as primer for new RNA synthesis by RDR. So infection continues... but this RNA can't be incorporated in Capsid in maturation phase! Who cares that? It is creating effective progeny, it is infecting its host, effectively stopping host translation... Fantastic Job! But the poor RNA itself dies with its host. An altruist.

Image Courtesy:
Poliovirus:
http://users.wfu.edu/banklm3/cell/index.html
Translation in Poliovirus:
http://pathmicro.med.sc.edu/book/virol-sta.htm

References:

1. Yuan Fon Lee et al., A Protein Covalently Linked to Poliovirus Genome RNA, 1977;74;59-63 PNAS oi:10.1073/pnas.74.1.59.

2. Akio Nomoto et al., The 5'-terminal Structures of Poliovirion RNA and Poliovirus mRNA Differ Only in the Genome-Linked Protein VPg, Proc. Natl. Acad. Sci. USA, Vol. 74, No. 12, pp. 5345-5349, December 1977.

3. Timothy J.R. Harris et al. Nucleic Acids Research, Vol. 8, No. 6, 1980.

4. Mason et al., Identificationand Characterizationofa cis-Acting Replication Element (cre) Adjacent to the Internal Ribosome Entry Site of Foot-and-Mouth Disease Virus, JOURNAL OF VIROLOGY, Oct. 2002, p. 9686–9694

12 hours and your cancer is cured!

Sometimes life is really tough. This entry was supposed to be in last Monday or Tuesday...

It's BAS. (Baizid Alam Shibib)

Last Monday, he came to the class and started day dreaming ;)

He was asking,"If someone from Bangladesh invents a drug which cures any type of cancer within 12 hours, will s/he get Nobel Prize?" I said,"Not once..."

How can a biochemist have such fantasy? When I told Tanaeem, he laughed and said,"This joker has no idea. Complications like cancer; curing in 12 hour! It is not a disease. You can't go and kill the pathogens! It's your cells dividing uncontrollably and bringing back the control requires hack of a time!!! At least couple of months, in fact years."

He could have increased his credibility! He could have said any particular cancer, may be in a month or 6 months... that would have made lot sense. All cancer! He has no idea how cancer forms. There are at least millions of ways: activation of oncogene, inactivation of tumor suppressor genes... non-functional cell signaling... mutation ... I don't think the list will ever end. And if someone says, he wants to treat all these with one and only drug (when I can't even list them in single sentence), then I guess he has problem in grasping the difference between cancer and other diseases... funny thing is he teaches Human Physiology in Department of Biochemistry. To add to the surprise list, Biochemistry students think he is the moving encyclopedia!!! Ha Ha Ha!

May be he meant Astrology's Cancer ;)

The Job of A Teacher

It was in DJ's class and I was bit confused about Physical Map of chromosome. Even though she didn't ask... it came up in my mind and I wanted to use this term. Yet I restrained. I had logics behind my idea. But I knew she wouldn't accept unless I'm right. Of course she is right in saying that I'm wrong. But not before hearing my explanations.

What's the job of a teacher? Is it just going to the class and deliver a pre-written speech like our President? I don't think so. Teaching is an interacting profession where your students are more important than you yourself. The most important part of teaching is developing your student's the quality of being critical to something, some ideas, concepts and developments. It's not like you go to your students, ask a question and reply, "Oh .... You are at the same place as yesterday."

I hate this rubbish educational system.

Image Courtesy: www.nature.com

A Brand New No and Puzzled SRK

Today's Topic: SRK. (For those who don't know, SRK stands for Sanchita Rahnuma Khan.)

Yesterday she was taking class on Horizontal Gene transfer between bacterial species, especially Transduction. As an intro she mentioned Zinder & Lederberg experiment. She told, in the experiment observed frequency of gene transfer between two auxotrophs were 10^-5. Anyway, she continued with her lecture. In the class I came to know following facts:

Firstly, the frequency of DNA transfer from bacterial genome to phage genome is 1-2 %.

Secondly, the frequency of DNA transfer from phage to another bacteria is 1-2%.

Taking these facts together, my calculation was the frequency of gene transfer would be 10^-4. The 10X anomaly can be explained if we consider the fact that each DNA transfer might not result in complete Gene transfer. But she gave another brand new data!!! She said, the frequency of gene transfer by transduction is around 10^-6. This was completely unexpected. I was wondering to solve the mystery of 10^-4 and 10^-5, instead a new data of 10^-6 came up. I was completely puzzled and brought the facts into her notice. To be honest, I asked her out of curiosity, I didn't mean to harass her. (If you are a teacher, I think you would prefer not to have me in your class ;). Cause I can create lots of troubles when I want to, and sometimes I do.) Felt sorry looking at her face and I myself tried to cover up things by answering from my instincts. Anyway, she told us to check things out.

I've downloaded Zinder & Lederberg's paper, read couple of pages. The paper is kind of clumsy, but I think I'll be able to figure it out...

Lamark and AAA

It's AAA today ;)

He was taking developmental biology. Nothing new, same old Triple A style. Suddenly I was stunned hearing some of his words!!! Was I hearing right? He said, memory is an important attribute in higher organism's cell... kind of Ok so far. Afterwards, as an example he said, experience from parents are passed to their offspring through cells. Gosh! Am I in 21st century? How can someone advocate Lamarkism which died in 19th century Darwinian Era? I should have argued with Akandh Sir. It's the old habit. I know there is no point. Critical thinking isn't appreciated in this failed educational system. Hail Memory! That's the only slogan here.

Another analogy which he wanted to draw appeared bit absurd to me. He said a shoe and an aeroplane manufacturing factory doesn't use the same material and technology. Likewise biologists expected distinct variation when they studied development of different multicellular organisms... but they were surprised to see the extent of similarity. Well, shoe and aeroplane are completely different things, their difference isn't even analogous to the difference between prokaryotes and eukaryotes. If he compared the production strategy of car and aeroplane, I think he would have found lots of similarities. The apparent similarity is at the same time a fascinating and a frustrating thing. Fascinating because it shows us the fundamental similarity, while it's frustrating because it testifies the fact that there are lots of to be discovered stuffs.

Meiosis: Who knows, me or DJ?

Net connection is awesome today.

I thought there was no DJ today, became surprised to see it was in the routine.

Today she discussed sex determination, chromosome, chromatin fibre, mitosis and meiosis. A question came in my mind when DJ was delivering her lecture. Why X and Y chromosome's are named so? I googled net and found the answer from Google books.

Q: Why X & Y chromosomes are named so?

Ans: A common misconception about X and Y chromosome is that they are named because of their shape. However, Hermann Henking named the X because it was mysterious, or exceptional in some way and that Nettie Stevens then simply continued the alphabetical sequence when she named the Y.

(Source: The X in Sex: How the X Chromosome Controls Our Lives By David. Bainbridge)

When DJ started mitosis and meiosis, I got confused whether she knows those terms or not?

Life starts through meiosis, after fusion of egg and sperm!!! I don't get any of this, especially when she is saying about Homo sapiens. (Her words are correct for haploid organisms who undergo meiosis when diploid zygote is formed.) I've to wait and see.

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Another confusion arose when she asked, "What is the difference between Chromatin fibre and Chromosome?" Different answers came from different corners. I think some of them were right, though weren't complete. Chromatin fibre is non-condensed string of nucleosome which divides and condenses before cell division. This condensed form of chromatin fibre is known as chromosome. (Appears H shape in typical karyotype). Anyway, DJ rejected them. Instead she accepted Maruf's lead (partially) which I found the least appropriate.

She also talked about Genetic Maps. I know there are three types of maps, but right now, I can't recollect.

DJ Siamese!!!

Toady DJ was taking class... she mentioned about Siamese Cat and related stuffs, the pigmentation pattern. One thing I found quite strange. She said, if we take a Siamese Cat to polar regions, it will turn into black completely! The logic was, since the temperature sensitive melanin producing enzyme (tyrosinase) will be functioning. I thought this was a rubbish idea.

Say we took a Siamese Cat to polar region (or incubated it in low temperature). If the mutant melanin producing enzyme had to function, the temperature of individual cells or tissues has to drop and more importantly the drop in temperature should sustain for a reasonable time (since melanin itself isn't mutant, rather one of melanin producing enzymes are mutant. You need time to synthesize melanin and make it express). This is quite unrealistic. In the extremities (or peripheral regions), the temperature is low. The reason being there is relatively low blood supply to exposed surface area ratio. High surface area is responsible for high heat loss rate, low blood supply amplifies the situation (Because blood is directly involved in temperature homeostasis). Theoretically in polar region, we may expect a Siamese Cat turn into completely black, but practically rapid temperature loss will lead to coma and eventually death long before you can see this bizarre hypothetical phenomenon.

Arguing with DJ has no point, those who know her personally will surely agree with me ;) .

Evolution, ID and Science

Those who say Evolution is unscientific, they have difficulty in grasping the beauty of Evolution.

But those who say Intelligent Design is scientific, they don't understand science at all.