What made HIV infect Man?

. Wednesday, August 22, 2007

About 4 million years ago, humans had split from apes. At this time, Chimpanzees had to go through some tough times. They were infected with a virus. Scientists discovered this when they found traces of this virus in the DNA of Chimps. This meant that this virus, called PtERV1, infected the Chimp population. Interestingly, the traces of the virus were not found in human genome.

Emerman and his team had an explanation. The humans immune to PtERV1 while Chimps had tough time fighting it. The team of researchers identified TRIM5 as the factor that helped humans protect us from the virus. Removing this protein from the cells made them vulnerable to PtVER1, which were reconstructed from Chimpanzees DNA.

Curiously, these cells were found to be less susceptible to HIV. It seems that in the process of developing resistance to one virus, the immune system of our ancestors had us vulnerable to another deadly virus, the HIV.

Journals Online

. Monday, August 6, 2007

Science knows no boundaries!

Here are a few websites that offer free access to some journals on the world wide web!!!

Current Science


Directory of Open Access Journals

Free Medical Journals

High Wire Press

PhysNet - Physics related free-access journals

If you know any other such useful websites, please do add those links as comments...

Making alcohol the nano way!

. Sunday, July 29, 2007

Ethanol (the alcohol) is one of the most talked about alternative for the fossil fuels. For thousands of years, alcohol has been produced from yeast. This way of using biological cells to make alcohol is not generally considered non-viable. Thats because we spend more energy than what we get.

Carbon Nano Tubes (CNTs) are tiny tubes made only of carbon atoms. These are too tiny that the properties of chemicals are often altered when they are in these tubes.
CNTs were found to catalyze the production of ethanol from carbon monoxide and hydrogen. CNTs act either as catalysts or catalyst additives.

In China, its been proven that CNTs loaded with Rhodium nanoparticles as reactors to convert the gas mixture of CO and Hydrogen into ethanol. Dr. Xinhe Bao and his team of researchers in Nano and Interfacial Catalysis Group in Chinese Academy of Sciences observed that the redox properties of metal nanoparticles are modified when they are inside CNTs.

Syngas (a mixture of CO and H2 in the ratio of 1:2) when introduced into the CNT loaded with Rhodium- Manganese catalyst, gets converted to acetaldehyde, acetic acid and ethanol very quickly. The Chinese scientists suggest that this is due to
1) a host guest interaction between CNT and Rhodium - Manganese nano particles.
2) stringent size restriction of metal particles inside CNT.
3) high affinity of H2 to the inner surfaces of CNT.

The DNA message

. Monday, July 2, 2007

You probably know that DNA carries the most invaluable information, without which the mere existence of life is impossible. Have you ever wondered whether DNA can be used to store more than just the genetic information? If you had thought of it before, you are not alone(!!!!!!).

A group of Japanese Molecular Biologists in Institute for Advanced Biosciences at Keio University decided to (nearly) immortalize Albert Einstein's magical formula E=mc^2 in the DNA of a bacterium.

DNA is a thread like molecule made of 4 different compounds (represented as A, G, C and T) as building blocks. The sequence of these 4 compounds in the DNA holds the genetic information. The Japanese scientists attempted to translate the formula (along with the year of its discovery, "1905") into binary code. This code was then translated into a language that has A, G, C and T as its 4 alphabets. For example, the binary code '0000' was translated into 'AA' and '0001' was indicated as 'CA'. Once the formula was translated into DNA's language (A,G, C and T), the new sequence obtained was inserted into a bacterial DNA and stored for eternity.

The objective here, was probably to preserve 'the most important formula of 21st century'. Since the genetic information had survived for over 3.5 billion years, DNA was the obvious choice. With the ability to survive in extremely hostile environmental conditions, the harmless soil bacterium Bacillus subtilis was a suitable candidate as the carrier of the "DNA-time capsule".

I hope that these efforts prove successful and Einstein's legacy (E=mc^2) lives on long after the demise of human kind on this planet.

Hmmmm....... I wonder what role the seemingly harmless equation E=mc^2 will play in the extinction of human population!


. Monday, May 28, 2007

The active components of the cone snail venom are a group of neurotoxins called conotoxins. These are usually 12 to 30 aminoacid residues long. The peptides are highly constrained due to high density of disulphide bonds.

Although conserved structures are present in these peptides there are also subtle differences. These differences are responsible for the high toxicity and high specificity. These differences also ensure that each species has a unique subset of toxins. It has also been found that sometimes, the toxins differ even among individuals of the same species.

The conotoxins present in the fish eating cone snails are more effective against humans than those present in the mollusk eating snails.

The cone snail venom causes paralysis. The paralytic conotoxins belong to three main classes: alpha, mu and omega conotoxins. There are also others ... delta and kappa conotoxins.

You will find a list of conotoxins here.

More of Cone Snails...

. Sunday, May 27, 2007

These amazing creatures are not only found in the deepest parts of the oceans but also on the shores. While the shell of the snail lets it camouflage and wait for the prey, its siphon provided with numerous chemosensors detects the prey that happens to linger dangerously close. The proboscis containing what is probably the most efficient hypodermic needle of nature loaded with the most potent concoction of dangerous toxins is ready for the prey.

The lack of physical agility of these seemingly lazy predators is well compensated by their lethal venom. Within seconds of injection of the deadly cocktail of some 100 different conotoxins, the victim immobilizes. The snail engulfs its paralysed prey and swallows it whole.

Click here to view an amazing video depicting just this.

Cone Snails

. Saturday, May 26, 2007

Have you ever wondered how those lazy small snails catch their prey?
Well, here is how they do...

Cone snails are some of the most amazing creatures in the world of marine animals. Very little is known about them. They have a mind-blowing variety of toxins. These toxins are usually about 12 to 30 amino acid residues long with unusually large numbers of disulphide bridges. The toxins are so diverse that no two species of cone snails have same toxins. Even the composition of different toxins in their venom differs.

The pharmaceutical potential of some of these toxins have been identified and are in clinical and preclinical studies. These toxins can be used in the treatment of various diseases, from hypertension to depression.

Toxin - Nanoparticle Combine Defeats Cancer

. Thursday, May 24, 2007

Diptheria toxin is a protein secreted by Corynebacterium diphtheriae.

The protein has three domains - A, B and T. The B domain is believed to be responsible for recognizing the cell surface receptors. The toxin is found to show affinity for heparin binding epidermal like growth factor like precursors, which are found on the cell surface. T domain aids the protein to gain entry into the cell.

The A chain has the enzymatic activity. It catalyzes the ADP ribosylation of eukaryotic aminoacyl transferase II. This prevents protein biosynthesis in the cells leading to cell death.

The diphtheria toxin A (DT - A) chain's toxic properties can be exploited by properly guiding them to the cells that need to be killed.

This is exactly what the researchers have done using nanotechnology.

A nanoparticulate system made of Poly(beta amino ester) polymer and poly( butane diol diacrylate co amino pentanol) was used to deliver the diphtheria toxin A (DT - A) gene. This gene is linked to a regulatory sequence that gets activated only in prostate cancer cells. While the specificity is taken care of by the gene regulator, safe delivery of the toxin into these cells is the responsibility of the nanoparticulate system. Now, the diphtheria toxin does the rest.

Studies in the laboratory show promising results. Well, I guess we can expect efficient nano based injectable or ingestible drugs to treat cancer in the near future.

Now Polonium...... then Ricin!!!!

. Wednesday, May 23, 2007

Alexander Litvinenko was assasinated in london recently. He was poisoned by radioactive Polonium 210.

Alexander Litvinenko had earlier accused the Kremblin of involvement in the death of about 300 people in Russia in 1999.

This is not the first time Russia stands accused of silencing its critics abroad through assassination.

In 1978, Georgi Markov, a communist defector was killed by a tiny pellet of a substance called Ricin.

He was Bulgarian. He took refuge in London and worked as a broadcaster in BBC. He criticized the Bulgarian communist regime. It is believed by many that this lead Bulgarian government to seek KGB's assistance in silencing him.

On September 7, 1978 he developed high fever and was admitted to the hospital. He died in three days. The cause of death was not clear. Before his death, he recalled an incident, which was key to unraveling this successful assassination attempt.

He was waiting at the bus stop near the Water Loo bridge when he felt a stinging pain in his legs. He turned and saw a man pick up his umbrella and apologize. He (probably) ignored it. But, by the time he realized that it was no accident, it was too late.

He died on September 11, 1978. During his postmortem investigation, forensic pathologists discovered a spherical pellet the size of a tiny pin-head. The pellet had two holes the size of 0.35mm drilled into it. Traces of Ricin was was found in those holes.

Ricin is a toxin. According to FBI, it is one of three most dangerous substances on Earth. It is perhaps the most easily available bioweapon.

Ricin is a protein found in the castor plant (Ricinus communis), the one from which we get Castor oil. This grows in almost all tropical countries. The toxic effects of castor seeds are well known.

Ricin is a very powerful cytotoxin. It belongs to a group of toxins called Ribosome Inactivation Proteins. Ricin is a Type 2 RIP. That is it has 2 poypeptide chains - one to bind to the cell membrane and the other to enter the cell and inactivate the ribosome.

The RTA chain of this heterodimeric protein gains entry into the cell with the help of RTB chain. Once inside, the RTA (a 267 residue long polypeptide) exhibits its N - glycosidase activity by removing A4324 in the 28S rRNA of 60 S subunit of the ribosome. Removal of this prevents the binding of elongation factors. This halts protein synthesis. The cell ultimately dies.

The toxic effects of this protein may develop as soon as within 2 hours of exposure. The symptoms of the ricin poisoning varies with the system that is exposed. It is quite difficult to zero in on the toxin very easily.

There is no vaccine for the protein. There is no direct cure. It is easily available and it is not that difficult to spot Castor plant in any country!!!

All these make it the most efficient bioweapon candidate. And, the 'umbrella murder' Georgi Markov brought the tropical toxin to the lime-light.


. Thursday, May 17, 2007

Here is another video on translation. Its amazing how a process can be viewed by different people in different ways. Well, as long as their imagination adds beauty to the actual process, I am thankful to the creator.

Nano in the Eyes

. Wednesday, May 16, 2007

At John Hopkins, researchers have developed a nanoparticle as a new biosensor to treat damaged retinal cells.

Biosensor detects oxidative stress inside the cells. It responds by regulating therapeutic gene expression. This reduces the damage caused by the free radicals.

Biosensor has an outer lipid layer. This layer also has some targeting proteins. These proteins recognize the endothelial cells lining the eye's blood vessels. The lipid outer layer ensures easy entry of the biosensor into the cell.

Once inside the cells, the DNA is exposed. If there is oxidative stress, the promoters are activated and two proteins are expressed. One, a fluorescent protein that helps in detection of the damaged cells; two, a therapeutic protein that reduces the damage.

They have tested the biosensor in animal models like mouse, rabbits, and dogs. These nanoparticles were also found to be nontoxic on cells but animals showed varied levels of toxicity.

You will find more info here.

why family

. Monday, May 14, 2007

If there is one change i want to bring about in the indian society, it would be to eliminate family system.


. Saturday, May 12, 2007

What an amazing video!!! This is one of the most spectacular videos I have come across that shows Life so beautifully that you just can't help but fall in love with it!

Oh yes! I'm talking about life inside the cells!!!!

Too desperate to get lucky!!!!

. Thursday, May 10, 2007

Luck!!!!! How strange it is!!! You try very hard to convince yourself that it does not exist. But, its simply not possible for you to ignore its apparent presence in every aspect of your life. Or so your lazy 'self' tends to believe.

I find myself in a state where I am just too desperate to get lucky. In definite need of some good luck...

Why would one need luck??? As far as my understanding goes, there can be two reasons: 1) You deserve to succeed in all ways and a bit of good luck would make your chances of winning a perfect 100%.
2)You have nothing that can get to the gates of victory and you need some good luck to get you there!!!
Now, if you know me, you will have no doubt which of the above reasons suits me best.

My observation of luck for the past 21 years is that it can be really tricky. Its too elusive when you look for it. You just ignore it, you will find yourself surrounded by it.

I wonder whether I am too desperate to get lucky!!!!

Translation Animated!!!

. Wednesday, May 9, 2007

Here is something I found on you tube! An interesting way of looking at the process of translation. Especially the aminoacyl tRNAs enter the ribosomes... Post transcriptional modifications were not given here. However, its a great piece of animation.

Flying Nano Wonders!!!!

. Tuesday, May 8, 2007

Butterflies are probably the most beautiful creatures on earth. Those colorful wings captivates you with its beauty.

Have you ever thought whether those magical patterns are formed by true colors??? In fact, these clever insects trick you into believing that their wings possess true colors. The wings have what can be called biophotonic crystals that scatter light in some intriguing ways. Something our 21st century physicists have hard time replicating in labs!

These are some ridges of nano dimensions found on the surface of the wings. These creatures have been exploiting the potentials of nanotechnology for the past 30 million years!!!!

What you see here is not some fabric... but the wings of a butter fly.

I found more details about this here. You may want to take a look at this site!

Fwd: Hmmm!!!!!

. Monday, May 7, 2007

Interesting!!!! Its interesting that I was not able to sign into this site...
Anyways, this gives me a perfect opportunity to test something! Posting through email. Let me see if it works....

Now, coming to the actual post...

Viroids were discovered very recently but they are believed to be present here on earth for as long as life itself! This was because of the fact that some of them exhibit hammerhead ribozyme activity.
They also have interesting way of replicating.......
I came across a mini review of viroids at sciencedirect.com . The paper was published in Febs Letters, volume 567, Issue 1, on 1st June 2004, Pages 42-48 .
Here is the link.



Virus - Proteins

. Saturday, May 5, 2007

Viroids are strange infectious agents. Intriguing and very interesting!

These are nothing but a piece (often a small one) of circular single stranded RNA. These viroids are just 250 to 500 bases long. What makes it interesting is the fact that they like prions defy the concept of cellular organisation!

These RNAs replicate by Rolling circle model of replication.

They are capable of infecting cells and cause diseases.
Many plants diseases are now known to be caused by various viroids.

These are found to exibit catalytic activity as well. Catalyses reactions like forming or breaking covalent bonds.

The only (?) human disease caused by viroids is Hepatitis D...

RNA interference

. Friday, May 4, 2007

Hi there! Here is something you will definitely like. The concept of RNA interference is explained in this video, I found in YouTube, very beautifully!!!!

. Thursday, May 3, 2007

If there is something in this world that never ceases to fascinate me is DNA. Especially, the fact that 6 ft of DNA is coiled into a compartment thats less than 3micrometre diameter. I found this amazing video on youtube. Enjoy!!!!!!


. Friday, April 20, 2007

Its not a new word. Its not a new feeling. Yet, it always takes you to a new level. You try to avoid it. But you know very well it will never let you run away from it.
Disappointments in my life has been as frequent as pot holes in Indian roads. But like a typical motorist, one tends to ignore it and move on. Sometimes, it shakes you up so hard, you need some time to realize that life is not over yet.
For some one who believes that everything happening in one's life has a reason, its quite difficult to understand what that reason could be. The obstacles I had been facing for the past few months needs to have a very strong reason. Guess, I will get to know that my the end of this summer........

not today!

. Tuesday, February 13, 2007

Why should one force himself to live in a way the society wants him to live????? Is it not possible to break out of the society????? If that means living alone in an deserted island with no contact to outside world, when am I going to find that island????????

break the rules - 2 Laugh to death

. Monday, February 12, 2007

In the early 1950's, New Guinea witnessed an epidemic. It was called 'Kuru' - laughing death. The individuals suffering from this disease laughed for no apparent reasons. Such a laughter indicated death.
In New Guinea, the Fore tribe were severely affected. So much so that their tribe was driven close to extinction because of this disease KURU which literally means 'trembling with fear'. It is a neurological disease. Other than untimely laughter, the individuals suffered from loss of muscular coordination, tremor, difficulty in walking, loss of memory and difficulty to swallow at various stages of the disease. It is fatal and one dies within 3 months to 2 years of onset of the disease. The infection may reside without any symptoms for 2 years to 30 years.

It was first suggested that this was a genetic disorder and when it was found to be infective, this was ruled out. But, the agent of infection remained mysterious.
By studying the symptoms, it was believed that the agent was a slow virus. This was proved incorrect when the real culprit emerged. The disease was caused by prions. The idea of a protein being an infectious agent was not something, many of the scientists studying the disease, thought of.

One of the customs of Fore tribe was that they believed in paying respect to their dead by consuming their corpses. This cannibalistic ritual lead to the spread of prions very easily and effectively.

When they finally gave up their unique way of showing love and respect for their elders, the spread of the disease was controlled and the disease was eradicated.

Stanley Prusiner, who studied prions and described its molecular biology received the Nobel in the year 1997.

break the rules-1

. Sunday, February 11, 2007

If there is anything that fascinates thats science. Especially, the human body. How complex is this machine????? It has been more than 10,000 years (since we started living a life that is different from other animals on the planet), still we are no where close to proclaim that our understanding of the magnificently complex 'human body' is complete.

Nature had always eluded human comprehension.

Discovery of prions toppled the perception that infectious agents are viruses or any living organisms. Prions are proteins that are capable of causing infections on their own.

Prions are thought to be misfolded proteins that once inside a cell, could cause the normal proteins to misfold and prevent the cell from performing their function.
The famous Madcow disease and Scrapie are caused by prions.

You can expect more posts on prions in the following weeks.


Security….. whats that?

. Saturday, February 10, 2007

I attended the University of Madras’ Sesquicentennial Year Commemoration lecture.

The security was impressive. When I saw police men in large numbers outside the university I had no clue which VVIP is going to come there. I was stopped by the security outside the university’s entrance. In spite of showing my ID card, he did not allow me in because I could not tell him exactly why I was there. It did not make me angry. Obviously, it was my fault. In fact, I was thrilled that I am going to attend such an important function. After a few of my classmates reached the place, we managed to convince him that we will pose no threat to the visiting VVIPs.

After gaining entry into the campus, we realized that we will not be allowed to enter the Senate hall, without an invitation. And, we did not have any invitation. We were asked to wait. Again. Meanwhile, I found a place under a tree. There were too many uniformed men and women. Curiously, none seemed to worry why we were standing there.

After some time, thanks to the a few class-mates’ enthusiasm, I found myself waiting to register outside the hall. After a few questions, I wrote my name down on the piece of paper provided to me wondering whether I need to sign. There was no time to ask such questions. I was stopped (again), at the entrance to the hall by two men. These guys looked just like those you find in movies. All that they lacked were a pair of sunglasses. It was a little dark there and that’s probably why they did not wear them. One of them searched me and checked my bag. Well, I did not expect that. When he felt something in one of the compartments of my bag, he got interested. He started taking out all the contents. I am no terrorist. There were just pens. Old pens, that is - all those that I found difficult to part with for the past six months and kept them well-protected in my bag. It was time to get embarrassed. He took out all those bits of paper – bills, photo covers, etc., that were in my bag. Then he found a calculator. The one I had been using for over 7 years now. (Now, you know…. I can’t let go of things I love). After checking whether it is some kind of a remote control by ……. Well, pressing some buttons randomly and finding out if anything blows up. There was no explosion. He proceeded to the main section of my bag. It had my water bottle in it. He checked the base of the bottle. That reminded me of some report I saw on BBC recently about the gadgets, the 21st century terrorists use. Did he think I could be a terrorist??????? Well, when that question formed in my mind, I could feel myself smiling.

Anyways, I was happy that they were doing all they could to keep the place safe.

After all that, I entered the hall. It was impressive. Not magnificent or spell binding, but impressive. I found a seat in the middle of the hall. I was able to check out the building properly from there. I had plenty of time to do that as we arrived 30 minutes before the VVIPs. At the beginning, I pitied for my lack of artistic intelligence to appreciate the art works there. After a few minutes though, I managed to find places where renovation was either incomplete or was so badly affected that efforts to renovate was not successful. I realized that the hall was no where close to perfection. The hall looked pretty small. Smaller than what I expected.

There was a mild music playing at the background as people settled down. It was nice. My attempts to identify the instrument used to create that music reminded me of my ignorance about music.

The PM arrived 10 minutes late. People in the hall became silent as soon as he sat down. But no one had any control over the noise from the beach road traffic. Now I realized that the hall was not the best place to listen to speeches. The echo in the hall made it very difficult for me to comprehend the PM’s accent. The silence in the hall also revealed the University’s mark - the screeching noise from one of the electric fans. Again, the echo prevented me from zeroing in on the source.

After the lecture, the PM was ready to be brainstormed. He took only a few questions. One interesting question was from a middle aged man who asked his question in a language that many like me assumed it to be Italian. He asked the PM about Italy recognizing India as a major tourist destination. The PM was generous and answered in his fluent English - or so that’s what I believe.

I did not find any security personnel at the entrance/exit. Fortunately, I did not have to go through that again.

What did I learn from this?

The Senate hall is not all that impressive!

What security check means!!!

Above all, before you go for some seminar/conference/function etc., find out what it is all about!!!!!!!!!!!!!!

. Friday, February 9, 2007

Hi everyone! Let me take you through the first 21 years of my life in the following few lines. I was born in Chennai, a city you’ll find near the southern tip of India on the world map. When I was born, it was called Madras.

The first few years of life were as unadventurous as it is now. I had to go through the ordeal of adjusting to a new school environment only once, that too when I was 12 or 13. Although I have some memories of that, it’s not worth sharing here.

Being identified as a calm and studious boy in school was not a good thing after all. During my childhood and in the early teens, I tried so hard to maintain this image and to avoid the tag of “trouble-maker” that I constantly suppressed my originality to please those around me. This includes teachers at school, parents at home. I didn’t do this consciously as I was of the idea that that’s what I was supposed to do. Well, I don’t regret that for it had molded me the way I am.

The assumptions that formed in those days resulted in the essential fabric of my ‘self’. I can’t elaborate on that for I’m still trying to understand what that actually means. And this blog is one of my serious attempts towards realizing that. Towards the beginning of this journey to realization. I had this irresistible urge to change this. But it wasn’t easy breaking away from the world. And certainly not possible to make a U turn. After a few adjustments here and there, I found a way out. I may not be able to create interest in things I ignored earlier but I can let myself follow my passions. When I can’t tell the world what I thought of something, I can certainly spend hours and hours thinking about it, telling myself. This may sound weird. But it does help. You learn to view things from different perspectives.

Having realized that I had taken an incorrect decision, I continued this journey without much satisfaction.

After I completed my final year at school, the fear of the mysterious and the unknown future began to tighten its hold on me. A few depressed weeks later, I got admitted to a college in Chennai itself. It wasn’t what I wanted. My dream of becoming independent remained one. And it still is. Change was not something I could handle easily. It’s almost always painful. Mentally. The college, though not very different from the school environment, was different in many ways. It took me a few months to get adjusted to the new subjects and the new environ. After three years at college, I found myself in a similar situation trying to adjust to a totally different atmosphere – the corporate world. Before I could settle down, I’m back with books, tests and exams.

Doing post graduation was the career step I wanted to take after UG. But, I didn’t have any subject in my mind. Now here I am, trying to master what is probably the most nascent field of science.

Hope this gave you an idea of who I am.

Gotta go now, Bye.


my first post!

. Wednesday, February 7, 2007

Oh, you are in my first blog.
Is blogging an alternative to the most unrestricted freedom - thinking????????
Well, let me look at this a little closer. Is it possible for me to blog everything that comes to my mind? Especially, when its about those I interact with everyday, those who affect my life in many ways and those who are likely to visit this page and read this?
It sounds outrageous. Outrageous... because one cannot be honest in a transparent forum like this. The reason.... well, there are more than one reason.
1. you simply can't hurt others.
2. Many a times you realize that your understanding of an individual is never complete.
3. You just can't afford to express your true thoughts about someone.

So, why am I here?
I love to experiment. Especially if it involves some kind of thinking for I am too lazy to do anything that involves real effort. From what I understand, blogging lets you think. It gives you an opportunity to voice your views without inhibitions (in most of the cases).
But there is probably one main reason why Im here. And, that is I want to be heard. The voice in my head is constantly heard by me. but. But, it simply does not exist beyond my imaginations, beyond my mind. This is an attempt to give words to those random voices, an attempt to cyber-immortalize those transient thoughts.