M Science

Cell

noreply@blogger.com (Unknown) — Thu, 23 Oct 2014 19:58:00 +0000

Nice animation. It gives you a short tour of the cell.

DNA Nanovases

noreply@blogger.com (Unknown) — Sun, 17 Apr 2011 16:16:00 +0000

Nanotechnologists from Arizona State University, USA have made "bowls", "flasks" and "vases" of nano-dimensions with nothing but DNA. This they have achieved using DNA Origami, a self-assembly technique where strands of DNA are folded and "stapled" together to make intricate structures just as paper is used in the conventional origami.

DNA is well-known for many decades as the molecule of life that holds all the essential information required for the formation and existence of an organism. However, its potential in nanotechnology has only recently been envisaged and is being realized now.

The amazing ability of one molecular strand of DNA to produce a regular double helix with another forms the essence of its structure and consequently its function. The same is used by chemists and biophysicts to make nanostructures with DNA. These structures may contain either a few strands of DNA connected to each other at various points to form various shapes and figures or, it may be a combination of a very long DNA molecule stapled together to produce a sheet, which is then folded (like in origami) to make structures. Sometimes, DNA molecules are also used as "smart glue" to create nanostructures with inorganic nanoparticles.

Several reports of DNA nanostructures have come out in the past few years. The most recent one is from one of the leaders from the field, Hao Yan at Biodesign Institute, Arizona State University. The group made circular rings of concentric DNA molecules of different sizes and placed them vertically one on top of each other and stapled them all together with tiny DNA molecules. The result of this simple-sounding tedious task was nanoflasks and nano-vases. The paper published in Science has the elegant structures captured by transmission electron microscopy and atomic force microscopy. It also has details of the experiment in the supporting information available on the internet probably for free.

What's special about this work is that a simple approach was demonstrated as effective in making three dimensional objects with smooth curvatures using DNA origami technique. It takes the field of DNA nanotechnology a great deal further towards the realization of fully functional devices.

Many believe that these nanoflasks can be made to carry medicine to the diseased cells, but that may take a while as the issues relating to the stability of these structures and the feasibility of their fabrication are yet to be addressed satisfactorily. Until then we should perhaps, wait for people to make DNA (or RNA) nanoflowers for these vases!

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Who says we are happy?

noreply@blogger.com (Unknown) — Sun, 09 Aug 2009 08:13:00 +0000

A recent study by Professors from University of Vermont has suggested that our happiness has increased by 4% in the last few years. The internet based study collected data from blogs and analyzed the mood of its authors. A Science NOW article reports the results that is to be published in the Journal of Happiness Studies.

Is this really a good news? I do not think so...

Its hard to understand the rationale behind this 'investigation'. This study seems to assume that majority of people in the world have access to internet and that the most favorite activity of people around the globe is blogging and writing songs and making it available to strangers on the internet.

It is probably right to say that blogs reflect the mood of an individual. However, it is grossly inaccurate to believe that blogs reflect just that. There are blogs about virtually everything including fictitious accounts of one's life. Using selected words to assess the emotion of the blogger at the time of writing can lead to false picture of his/her state of mind. This is highly error-prone when the group under study comprises of young people who find it fashionable and trendy to use words that hold "dark" emotional values.

Have the scientists tried to analyze content from other languages? English is certainly not the only language people use. Neither is it the language used by majority of people in the world. This study is very clearly US-centric. It says, "The happiest day since 2005 was 4 November 2008, the U.S. presidential election, with a score of 6.3." While the population of United States hardly constitutes a major chunk of the world population, the number of people who find this news sensible is likely to be far too less and its incorrect to say that this study reflects the 'mood' of the world. I believe this is true even if one considers only those who use internet regularly.

The views of the professors are equally 'regional' in its implications and can never be extrapolated to the real world out there!

Bringing Back the Light

noreply@blogger.com (Unknown) — Wed, 05 Aug 2009 18:19:00 +0000

Glaucoma is a condition where the fluid present in the eyeball exerts too much of pressure onto the cells of retina causing the retinal ganglion cells to die. If left undetected/untreated, it causes blindness.

Progressing Darkness - Through the eyes of a glaucoma patient
It is the second cause of blindness in the world. In addition to this, there are 2 reasons why one has to take this with utmost seriousness:

It is known as 'sneak thief of sight' because people lose sight slowly and almost unknowingly. Often, it becomes recognizable only at the advanced stages.
The damages to the optic nerve fibres are irreversibile.

This was the case until now...
If what a group of researchers from University of Rome are claiming is right, it will be possible to help revive the damaged retinal cells of the patients suffering from this painful disease. That too without having to undergo more painful therapeutic procedures or surgery but with just a few drops of an NGF - Nerve Growth Factor.

They have discovered that administration of NGF in the form of drops directly in the eye produces a considerable reduction in the damage caused to the retinal ganglion cells by increased intr ocular pressure. After success with rats, the same experiment was tried with humans. Amidst concerns about the soundness of the experiment and its interpretations, the neuroscientists have claimed that this works with humans as well.

While scientists debate on the authenticity of the results and the need to indulge in verifying the claims, one can only hope that this simple solution to this dangerous disease guides research leading to achieving the ultimate reversibility - bringing back light into the life of many of its victims!

Do They Taste Light?

noreply@blogger.com (Unknown) — Tue, 05 Aug 2008 19:10:00 +0000

My previous post was about the fact that C.elegans were sensitive to UV light. What made this more interesting was the protein that was discovered as responsible for this special character.

Conventional studies in these nematodes by Stacey L. Edwards, Kenneth G. Miller, and colleagues allowed them to identify a protein as being behind this interesting property. They called it, lite-1. Curiously, this protein was very similar to those that were known to be involved in tasting. Further investigations established that lite-1 did act as receptor for UV light.

This protein may soon find its way to the tool box of the modern molecular biologists. Perhaps, this protein also shows that there may be other proteins in higher organisms that are waiting to reveal their secrets!

Things are not what they seem to be... especially in the world of biology!

Seeing Light Without Eyes

noreply@blogger.com (Unknown) — Sun, 03 Aug 2008 16:55:00 +0000

Many of the ground breaking discoveries in molecular developmental biology were made with the help of simple organisms that can be grown in laboratories with ease. Caenorhabditis elegans is one among them. Measuring about a millimeter in length, these organisms had been a good friend for molecular biologists and neuroscientists for decades. One reason why a common man may find this kind of round worm interesting is that they managed to survive the historic Columbia space Shuttle disaster. (Find more information here.)

These survivors are continuing to surprise their masters and challenging the claim that their physiology is well-studied. Not many would have expected these underground creatures to show any interest in light. Shawn Xu, a neurobiologist from University of Michigan proved just that. Upon observing that these creatures shy away from bright light while he viewed them under the microscope, he set out to explain how these eye-less worms see light.

Further investigations by Xu and his team revealed that four pairs of sensory neurons of C.elegans were responsible for its sensitivity to light. And, these neurons made them reverse their course as soon as the light is switched on.

(Find a more detailed article in ScienceNOW)

It was also found that these worms were more sensitive to the harmful UV-A radiations. This gives a clue to why evolution had gifted these simple organisms with this ability. Without these four neurons and hence the perception of light, the organisms may wander out into the light and get exposed to the harmful radiations. Such behavioral responses to light in such simpler organisms is more crucial to an evolutionary biologist, trying to understand the how higher vertebrates evolved sight.

DNA Crystallization in vivo

noreply@blogger.com (Unknown) — Thu, 13 Mar 2008 17:15:00 +0000

Bacteria are some of the marvelous creations of nature. They are known for their adaptability. The humble Escherichia coli that we find in almost all the microbiology and molecular biology labs continues to surprise us with its ingenius ways of handling problems.

Under extreme stress, bacterial cells are known to take many steps to protect themselves. Abraham Minsky of the Weizmann Institute of Science in Rehovot, Israel identified an interesting defense mechanism of E.coli thats slightly different. These unicellular organisms crystallize their own DNA.
This 'novel' defence strategy was found to be the responsibility of a protein called Dps. It resembles ferritin, an iron-storage protein found in humans.

Dps is produced when the cell experiences nutritive or oxidative stress. It binds to DNA (apparently without any specificity) and promotes its crystallisation. Earlier investigations revealed another important function of the Dps protein. It sequesters iron and other metal ions that may help in the generation of free-radicals.

DNA - Dps crystals

Minsky and his collegues genetically engineered a few bacterial cells to over-produce this protein. These cells formed DNA crystals more easily and starvation was sufficient to cause crystallization of DNA. This process was also found to be reversible. "Once nutrients are supplied, [the crystals] disappear within a very short timescale, and the bacteria are viable and growing," says Minsky.

Whats remains to be explained is, how the bacterial DNA integrates itself into a crystal!

Stretching DNA on a chip

noreply@blogger.com (Unknown) — Fri, 29 Feb 2008 18:52:00 +0000

DNA carries all information a living organism requires for survival. Reading this information can be made much easier if you can get these 2nm wide polymer strand stretched and untangled. Researchers at Purdue University have done just that.

They have precisely placed strands of DNA on a silicon chip and then stretched out the strands so that their encoded information might be read more clearly. This may prove extremely critical in future electronic devices and computers.

Find more information here.

What made HIV infect Man?

noreply@blogger.com (Unknown) — Wed, 22 Aug 2007 17:39:00 +0000

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

noreply@blogger.com (Unknown) — Mon, 06 Aug 2007 17:51:00 +0000

Science knows no boundaries!

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

Current Science

BioMedCentral

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!

noreply@blogger.com (Unknown) — Sun, 29 Jul 2007 17:04:00 +0000

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

noreply@blogger.com (Unknown) — Mon, 02 Jul 2007 17:14:00 +0000

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!

Conotoxins

noreply@blogger.com (Unknown) — Mon, 28 May 2007 20:02:00 +0000

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...

noreply@blogger.com (Unknown) — Sun, 27 May 2007 22:02:00 +0000

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

noreply@blogger.com (Unknown) — Sat, 26 May 2007 20:37:00 +0000

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

noreply@blogger.com (Unknown) — Thu, 24 May 2007 19:18:00 +0000

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!!!!

noreply@blogger.com (Unknown) — Wed, 23 May 2007 20:45:00 +0000

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.

Translation

noreply@blogger.com (Unknown) — Thu, 17 May 2007 19:05:00 +0000

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

noreply@blogger.com (Unknown) — Wed, 16 May 2007 18:19:00 +0000

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.

LIFE!!!!

noreply@blogger.com (Unknown) — Sat, 12 May 2007 20:41:00 +0000

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!!!!

noreply@blogger.com (Unknown) — Thu, 10 May 2007 17:32:00 +0000

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!!!

noreply@blogger.com (Unknown) — Wed, 09 May 2007 19:56:00 +0000

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!!!!

noreply@blogger.com (Unknown) — Tue, 08 May 2007 19:14:00 +0000

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!!!!!

noreply@blogger.com (Unknown) — Mon, 07 May 2007 16:50:00 +0000

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.

http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6T36-4C8DD9G-2&_user=10&_coverDate=06%2F01%2F2004&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=e491b0abfc3ed8806012a7ad81c01ee2

--

Virus - Proteins

noreply@blogger.com (Unknown) — Sat, 05 May 2007 19:53:00 +0000

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...