Restriction Enzyme

Restriction enzymes are important tool for molecular biologists. As far as I know, these enzymes are solely found in Prokaryotic System... Is there any Eukaryotic Restriction Enzyme?

If you know any, please put the name and its source in the comment box.

Enjoy your time.

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.

(Right click and open in new window or tab to view enlarged image)

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.

Ignorance Vs Truth

I am shocked!!!! This is a victory of ignorance and bureaucracy over truth. I am amazed to see the naturte of allegation; 7 years back... I've enough doubt whether the development of genetic engineering was as advanced to engineer HIV virus!!!- That's what the lawers of the patients said. Funny logic indeed.

Initially Libya contacted Luc Montagnier, the co-discoverer of HIV virus, to conduct inspection of the mass outbreak of AIDS. Luc Montagnier's report cleared the Palesteinian Doctor and Bulgarian Nurses, instead he accused dirty condition of the Libyan Hospital (which is considered one of the best there). Libyan court rejected the report citing the report contradicted Libyan doctor's initial report. - What an idiotic reason behind rejecting!!!

There is still an option of appeal. Hope the court will uphold Justice....

Below goes the news from Yahooo News:

Libya sentences Bulgaria nurses to death

By KHALED EL-DEEB and WILLA THAYER, Associated Press Writers

TRIPOLI, Libya - Five Bulgarian nurses and a Palestinian doctor were convicted and sentenced to death by a Libyan court Tuesday on charges they deliberately infected hundreds of children with the
AIDS virus. The verdict can be appealed.

Judge Mahmoud Hawissa read out the verdict at a seven-minute hearing in a Tripoli court at the end of the defendants' second trial.

The six defendants, detained for nearly seven years, had previously been convicted and condemned to death, but Libyan judges granted them a retrial after international protests over the fairness of the proceedings. Bulgaria contends the children were infected by unsanitary practices at their Libyan hospital.

An international legal observer, Francois Cantier of Lawyers Without Borders, criticized the retrial as lacking scientific rigor. Research published this month said samples from the infected children showed their viruses were contracted before the six defendants started working at the hospital in question.

"We need scientific evidence. It is a medical issue, not only a judicial one," Cantier said after the verdict.

The long trial of the six foreign medical workers has become a bone of contention in Libyan leader Moammar Gadhafi's efforts to rebuild ties with the West. Europe and the United States have called for their release, indicating that future relations with Libya would be affected by Tuesday's verdict.

But Libyans strongly supported a conviction. Some 50 relatives of the infected children — about 50 of whom have already died of AIDS — waited outside the court early Tuesday morning, holding poster-sized pictures of their children and bearing placards that read "Death for the children killers" and "
HIV made in Bulgaria."

When the Supreme Court ordered a retrial in December 2005, friends and relatives rioted in Benghazi, the Libyan city where the children were infected in a state hospital.

Bulgarians will no doubt be disappointed by Tuesday's verdict. Hundreds of people staged peaceful protests in support of the five nurses in Bulgaria on Monday.

Europe, the United States and international rights groups have accused Libya of prosecuting the six foreign staff as scapegoats for dirty conditions at the Benghazi children's hospital.

Luc Montagnier — the French doctor who was a co-discoverer of HIV — testified in the first trial that the virus was active in the hospital before the Bulgarian nurses began their contracts there in 1998.

More evidence for that argument surfaced on Dec. 6 — too late to be submitted in court — when Nature magazine published an analysis of HIV and hepatitis virus samples from the children.

Using changes in the genetic information of HIV over time as a "molecular clock," the analysts concluded that the virus was contracted before the six defendants arrived at the hospital — perhaps even three years before.

Idriss Lagha, the president of a group representing the victims, rejected the Nature article, telling a news conference in London on Monday that the nurses had infected the children with a "genetically engineered" virus. He accused them as doing so for research on behalf of foreign intelligence agencies.

When the defendants were allowed to give evidence last month, they denied intentionally infecting children.

"No doctor or nurse would dare commit such a dreadful crime," said nurse Cristiana Valcheva, adding that she sympathized with the victims and their families.

A second Bulgarian, Valentina Siropulo, testified that of her seven years in Libya, "I've spent only 6 months working as a nurse and the rest of the time in prison."

Gadhafi, who has been trying to refashion his image from leader of a rogue state, got his government to ask Bulgaria to pay compensation to the children's families.

But Sofia rejected the idea as indicating an admission of the nurses' guilt.

Missing Communication

Last night, I was going through pages of Plant Physiology by Ross & Salisbury. I came up with a box entitled “Must We Write?” by Page W Morgan. The objective was why and how to write? It was in interesting comprehension in terms of both content and purpose.

It’s not surprising to me when I found the box stating that most of the science students find writing and communicating rather a useless time spending (which view I used to hold as well ;)). He put down some arguments against this. I think he was quite clear in his points.

I don’t like verbal communication with lots of people in general. But not sure what would be my attitude if the subject of communication is unknown to most of the listeners (Somehow I’ve the feeling that I will enjoy then.) But writing stuffs was never that irritating and boring to me.

Reading that article, I felt we miss one thing badly here in Bangladesh. It’s the lack of opportunities in developing communicating skills. There isn’t much we can do as students. In our department, DJ is trying to do something new. But I don’t like her approach. Anyway, everyone has his/her own style. We must learn to respect others. That’s one of the things we all have to learn.

Folding or Misfolding???

I's thinking about protein folding... there are terms like misfolding, unfolding and folding.

Misfolding is kind of misleading term. As far as I remember in Biochem texts Misfolding refers to 3D arrangements other than native conformation. Then what's the native conformation??? You'll asnwer the conformation that's found naturally... more or less that's the prevalent concept.

I've problem in accepting the word Naturally. I think each and every protein has millions of naturally occuring confoormations... even if the sequence of amino acids is identical (after all the melieu isn't identical) . What you're referring as Misfolding today might appear to be the most abundant fold... We don't have what's going through most of the life forms.

Instead of Misfolding we should use Variations of Folding Pattern.

Human mind is like proteins also. There are lots of ideas, concepts, thoughts... and most importantly they are environment dependent. The view you're holding today might be well differnt from the view of tomorrow's you.

That's enough for explaining the Title of my Newest Blog.