Science Simplified!

Monday, July 28, 2014

RotM: Interview with Dr. Justin Boddey


As part of our continuing effort to bring to you the latest developments in the field of science, we are proud to introduce a new section to our blog, Researcher of the Month (RotM), where we will speak about ground breaking research findings and to the researchers behind the work. 

In our first RotM interview, we spoke to Dr. Justin Boddey, a researcher at the Infection and Immunity Division at the Walter and Eliza Hill Institute, Australia. Dr. Justin recently published his findings regarding Plasmepsin V in PLoS One, which has shed new light on our understanding of malarial parasite, Plasmodium, and how we can prevent its spread. 
Here's Dr. Justin telling us more about his findings. 



CTS: For the benefit of our readers, please tell us about the fresh perspective that your recent findings have provided to tackling malaria.
Dr. Justin Boddey in his lab at WEHI
JB: Malaria parasites are very clever; they invade red blood cells and change them by delivering more than 300 proteins into them. This is required for the malarial parasite to survive in our body but this is also what makes people feel sick. We have developed a drug-like compound that blocks a parasite enzyme, called Plasmepsin V (PMV), which controls protein delivery into red blood cells. This prevents malaria parasites from sufficiently changing the cells and they die.


CTS: How does the compound that you have developed block PMV?
JB: We developed PMV inhibitors, called WEHI-916, by copying the general shape of malaria proteins that PMV can recognise. The inhibitors bind to PMV and block its activity due to which malaria causing proteins cannot be transported correctly. If you think about PMV as a lock in a door, we developed a very small key that fits inside the lock and blocks any other key from gaining access. So the lock is now useless, and nothing can go through the door.

CTS: From your publication, we have found that WEHI-916, has a small window to be effective (20-30 hours after erthyrocyte invasion). How do you envisage the inhibitor to be successful in treating malaria?
JB: Actually, the inhibitor WEHI-916 blocks protein transport very early in the parasite's lifecycle. However, it takes some time for the parasites to die from the blockage. Many antimalarial drugs have a specific window of activity, so this is not a big concern. Compounds based on WEHI-916 could be useful for prophylaxis, in addition to treatment of malaria.

CTS: What happens next? How does WEHI-916 become a drug against malaria?
JB:The development of WEHI-916 is the first step toward a new drug. However,  WEHI-916 cannot become a marketable drug. It is a peptide. Its value lies in the demonstration that inhibition of Plasmepsin V kills the parasite. So future drugs that have the same activity would be possible drugs. We aim to work with people like the Medicines for Malaria Venture (MMV) to help in development of the drug and take it through clinical trials.

CTS:What are the hurdles when it comes to combating infectious diseases such as malaria?
JB: Drug resistance is a major hurdle since parasites evolve to overcome drugs that are effective against them. So, we have to constantly work on identifying new targets that may be suitable for inhibition by antimalarial drugs. For this, we study the molecular mechanisms underlying essential processes in parasites, such as how they survive inside the human cells they infect. That is why the demonstration that PMV is a valid antimalarial drug target is so exciting.

CTS: Of all diseases and disorders, why did you choose to study malaria?
JB: Malaria has plagued humans for over 100,000 years and is still an enormous global health problem today. So I believe it is a very important cause. I am also fascinated by the way malaria parasites manipulate their human host to ensure their own survival and am driven to understand this at the molecular level.




Tuesday, July 22, 2014

Living with malaria


Everyone in India, at some point in their lives, may have been infected with malaria. Now this may sound a little out there, but may not be something far away from reality. Just recently, Times of India reported that 67 people died in Tripura of malaria in the last month alone, and 55 among them, were children. The north eastern state of our country is amongst one of the most gravely hit regions when it comes to malarial outbreaks, along with the other red zone regions, Andaman and Nicobar islands and Pondicherry. 

Malaria has been around in India for quite a while now. In fact, the discovery of its vector- the mosquito was done here in India by Sir Ronald Ross who bagged the Nobel Prize in Physiology and Medicine for his discovery. There are about 250 million people affected every year with the malarial parasite, out of which nearly 2 million succumb to the disease. In India, alone we face a daunting number of around 30,000- 50,000 deaths caused due to malaria each year, most of them being children. This is very different from what is officially released by the government which is hugely down playing the numbers to a mere 1,023 deaths in 2010 and 440 deaths in 2013. (True number of malarial deaths in India)

But it is not just recently that the malarial parasite has been causing havoc. Estimates are that the malarial parasite, Plasmodium, is the single most deadly organism known to the human race. If numbers are to be believed it has done more damage to humanity that any war, or natural calamity, making it the deadliest parasite ever. Vasco da Gama, Genghis Khan, Alexander the great are just a few names out of the many who succumbed to the malaria.

Since the dawn of humanity itself, malaria, has been at the periphery of our existence. The first documented case of malaria comes from Hippocrates, the father of medicine, who described the symptoms. It is believed that the co-relation that was made between stagnant water and the spread of the malarial disease, prompted the Romans to build the drainage system. But the very fact that the parasite has been around for a while and managed to survive changes in its environment says quite a bit about its evolution, doesn’t it?

In the past, we had effective drugs to curb the disease, but the parasite soon grew resistant to the drug, which is why even today, we face a threat that malaria might turn into a global pandemic. Arteminisin, has been one of the most effective drug developed against the malarial parasite till date. But recently, cases in Cambodia have surfaced, where in the most deadly of the malarial strain- Plasmodium falcipuram, has shown resistance to the drug. This is not only an interesting development; in terms of evolution, but also in terms of global health, where there can be absolutely no sure shot way we could combat the spread of the disease.

But this is not where the weirdness of the evolution and smartness (if I may add) of the parasite ends. Researchers at the Pennsylvania State University have observed that infection of Plasmodium in hosts that have been exposed to some malarial vaccines before results in the parasite launching a deadlier attack on the host. This is not to say that the parasite comes up with some novel way of attaching the host, it simply multiplies more aggressively, overwhelming the host immune system rendering the vaccine useless. The parasite even manages to modify its vector, the mosquito's behaviour, who show greater affinity for human blood, after being infected by Plasmodium. 

Luckily, the evolutionary adaption is not just one sided. According to a malaria hypothesis, put forth by J. B. S. Haldane in 1949, the prominence of red blood cell disorders, in the tropical regions was an indication of natural selection at work. Red blood cell disorders like sickle cell anaemia and thalassemia discourage the infection of red blood cells. This was later confirmed by A.C. Allison who showed that the mutation in the sickle cell mutation (in the beta hemoglobin gene) was geographically confined to Africa, where malaria is most wide spread. 

But the bottom line remains, that even though we seem to evolve ourselves and our methods to combat malaria, the rate at which the plasmodium is evolving is much faster and we need to come up with a better understanding of the parasite and novel techniques to combat the disease.

For the interested reader, here is an interesting Ted Talk from Prof. Andrew Read on Evolutionary Medicine.


Tuesday, July 15, 2014

Fish on Wheels

7:21 PM Posted by Editor CTS , , No comments
For all those who pet lovers, who would love their pet fish to be with them at all times, Studio Diip, a Netherlands based startup lets you buy a unique aquarium that will let your fish steer in any direction it wants.

By using advanced computer vision technology, entrepreneurs at Studio Diip, were able to design an aquarium with wheels which moves in the same direction as the fish moves in the tank.

Here is the video of how the technology works!




Unfortunately, the company could not find enough investors for this crazy idea and the project has been stalled for a while. But in case you have deep pockets and the zeal to let your fish drive around the house, do contact the team at Studio Diip to get this project started once again!

Wednesday, July 9, 2014

Can you hear a caterpillar munching on leaves? Well, plants can!


Image source: Wikimedia
How often have we seen a caterpillar silently eat away an entire leaf of a plant to feed its hungry stomach. What if we told you that every time you thought the plant was helpless against the over-eating caterpillar, you were wrong? A recently published study in the journal Oecologia tells us that plants can actually hear the tiny vibrations that the caterpillar emits whilst feeding and prepare themselves for a similar event if it occurs in the future. Sounds interesting? Read on!!! 

We have all heard of tales where listening to soothing music (acoustic energy or sound) has helped plants grow. But researchers, Heidi Appel and Reginald Cocroft at the University of Missouri, set out to investigate how plants responded to sounds that were relevant to their survival. To test this, the researchers allowed caterpillars to feed on Arabidopsis plant, while they recorded the vibrations of the leaf during the process of feeding with the help of a laser. 


Video source: MU News Bureau

The recordings were then played to set of plants (lets call them Set A) while another set of plants (Set B) were played something like a blank cassette. Later on, caterpillars were allowed to feed on both these plants and interestingly, Set A plants recognized the vibrations that were reaching them now and started producing more mustard oils, a compound that deters the caterpillars from further feeding and naturally caterpillars crawled away. What the researchers found even more interesting was that the plants were able to differentiate the sound of feeding caterpillars from that of say another winged insect or leaf fluttering due to wind. 

While further research is needed to understand how exactly plants perceive these vibrations and respond to them, the initial findings offer a glint of hope in the years to come, we will move away from our dependence on insecticides! 

If you enjoyed reading this article, you might also like our article about how maize plant attacks its herbivore pest.   




Wednesday, June 4, 2014

The Sound of Music!

English: Major chord in root, first and second...
English: Major chord in root, first and second inversion.
(Photo credit: Wikipedia)
Music is one of the most mysterious entities in the world of science. Food for your brain, but how does it work really?

I am a conservative when it comes to what kind of music I like listening to and what I presume would make me cringe. Now because I am from India, have lived in UAE and done a wee bit of roaming around the globe, I like to say I have a wide spectrum of sounds I find very pleasant.  But having said that, there are styles of music that I’d rather not venture into, and they do make it to my “no way I can ever listen to this” category.  

But a recent article forced me to listen to some pieces that although are clear candidates of my ‘cringe worthy’ music category, I really loved a few of them, and they, and in extension a few others in the category, have been regulars on my playlist off late. This really got me thinking, about how arbitrary my definition of what I find unpleasant in music really was, which further got me thinking, how arbitrary music really is, how little we know about it.

For starters, there is nothing tangible in it, a series of harmonics put together to make a longer sound. Anthropologists say that music brings together a community, binding people into one culture. Archaeologists have found some of the first musical instruments, dating back to over 57000 years, which were, even back then, fine-tuned to perfection, stating, that even then primitive man head banged at some foot tapping tune. Now that is profound!

It is believed that we like to listen to music that falls in our acoustic and vocal range. We like listening to beats and tempos that are very close to our own heartbeat. So, one may point, that music appeases the primitive side of our nature. So does this apply to other creatures, apart from us?

Well yes, studies show that music is not only restricted to the human race. Animals, too, like to listen to music, but whether theirs is what we term as ‘music’ has scientists divided. While primates like to listen to slow tempo, they are not very enthusiastic about thewhole idea of music. On the other hand however, cats and dogs prove to be at the other end of the spectrum when it comes to music. But contrary to what many pet owners believe they don’t particularly like human music. Cats swing to a song that is in tune with the frequency at which they vocalise.  In fact, a company by the name of ‘Music for cats’, sells these ‘cat tunes' online. Dogs seem to have a keen ear for the right pitch. 


But there are animals that are not just passive listeners, but musicians themselves. Humpback whales produce sounds that are closely related to the music format, we humans listen to. So in essence, a phrase, that is followed by a new one after which the old one is repeated, sounds familiar? Even birds are known to follow similar rhythmic rules when it comes to their songs. In fact, birds are known to produce songs that are in tune with human music with addition of percussion elements as well.

But do animals enjoy what they are listening to, or have any emotional response to music the way we do? Well recent studies prove that they very much have the perception of music being pleasurable, hence being able to enjoy music. In a study, in 2001, scientists in UK, looked at the effect of music on cows, and it was observed that while playing bits that were of a beat rate of 100 or lesser, cows produced up to 3 % more milk as compared to no music at all, and playing anything higher than that would result in a drop of milk production.

While there are growing revelations on whether animals like music or not, there are a few revelation of our own that we are just coming to terms with, like, not every one likes music, or has a pleasurable response to music. Scientists call this, Anhedonia, the inability of an individual to experience pleasure from an otherwise pleasurable activity- like music. And anhedonia seems to be fairly wide spread in the population. These people seems to process other reward based activities normally, music however, does not act as a reward for them. They don’t connect to music the way many people do. So the next time you have someone, saying they don’t get it- musically, don’t blame them.


Below are some links that I thought our readers would find interesting. 

Questionnaire on music http://www.brainvitge.org/bmrq.php


Tuesday, May 27, 2014

5 reasons why 'Three Person IVF' is not really worth the trouble?

The introduction of 'In vitro fertilization' technique in the field of reproductive medicine came as a boon for thousands of couples who, until then, were left helpless by their inability to conceive. The hard work of Patrick Steptoe and Robert Edwards in developing this technique bore fruit in 1977, when Lousie Brown, the world's first 'test-tube baby' was born in Manchester.

This moment in history was glorified recently in the year 2010, when Edwards was given the Nobel Prize in Medicine. By now, the technique had helped thousands of families all over the globe and become simply known as IVF to one and all. But within a few years from this glorious moment, we are looking at yet another breakthrough in reproductive medicine, which goes much further than what IVF achieved. Instead of just fertilizing the eggs in a petri-dish, a 'The 'Three Person IVF' allows for fertilization of an egg, using DNA from three people, the father, the mother and a donor. The UK is pushing the draft of a regulatory framework that will allow them to become the first country to allow 'Three person IVF'.

How different is 'three person IVF'?

Normal IVF


In a normal IVF, the egg  (containing nuclear as well as mitochondrial DNA) from the mother and the sperm (containing nuclear DNA) from the father is usually taken in a petri-dish to facilitate fertilization. In case, the egg or the sperm is faulty, an egg or a sperm donor steps in (replacing the previous provider) and helps in the fertilization process. Fertilized eggs are then implanted in the woman's uterus, marking the beginning of her pregnancy.


Three person IVF


A 'three person IVF' will be taken up, when the mother has a mutation in her mitochondrial DNA that prevents the foetus from being healthy at birth. Since the mitochondrial DNA is present only in the egg, a donor will step into the picture, where in she will donate her egg, from which the nucleus will be removed and then be replaced by nucleus from the mother's egg. The resultant embryo that will be formed post in vitro-fertilization, will have nuclear DNA from both the father and the mother and mitochondrial DNA from the donor, thereby making this procedure a three person affair.



While this might be welcome news for women who happen to have mitochondrial mutations and cannot conceive normal healthy children, the question we need to ask is whether a 'three person IVF' is actually any significant development as such?

1. First and foremost, IVF, by itself, is a laborious process, especially for the mother, with a fair chance for failures. Since a three person IVF requires two egg donors, two women now, need to undergo the procedure.

2. IVF is not an easily affordable procedure. The addition of another person to the procedure, means additional medical expenditure for the couple or the state (depending on your location and the nature of medical services therein).

3. One simply cannot find a reason to justify this 'Three-person IVF', since the already existing option of a regular 'two person IVF', is also going to bear the same result - a foetus free from any deadly mitochondrial disease.

4. Our recent post on mitochondrial numts spoke on how mitochondrial DNA imprints itself on the nuclear DNA as well. In case of a 'Three person IVF,' the mitochondrial and nuclear genome are not going to be from the same person. Would this have any impact on the health of the foetus, is something, we need concrete data on. Certain studies have been done in chimps but the data was not really (a, b, c) conclusive and a thorough examination is still needed in this regard.

5. There is hardly any cutting edge technological development that is happening with a three person IVF. It is simply a matter of 'cutting and pasting' of the nucleus from one egg to another. If the researchers had managed to find a way to silence the mitochondrial mutations, that would be of real great help. Knowing how to do this, 'cut & paste' of nuclear genome, might be good from an academic viewpoint but rushing to do for a patient is not really necessary.


a. Tachibana, M., Sparman, M., Sritanaudomchai, H., Ma, H., Clepper, L., Woodward, J., Li, Y., Ramsey, C., Kolotushkina, O., & Mitalipov, S. (2009). Mitochondrial gene replacement in primate offspring and embryonic stem cells Nature, 461 (7262), 367-372 DOI: 10.1038/nature08368

b. Tachibana, M., Amato, P., Sparman, M., Woodward, J., Sanchis, D., Ma, H., Gutierrez, N., Tippner-Hedges, R., Kang, E., Lee, H., Ramsey, C., Masterson, K., Battaglia, D., Lee, D., Wu, D., Jensen, J., Patton, P., Gokhale, S., Stouffer, R., & Mitalipov, S. (2012). Towards germline gene therapy of inherited mitochondrial diseases Nature, 493 (7434), 627-631 DOI: 10.1038/nature11647

c. Lee, H., Ma, H., Juanes, R., Tachibana, M., Sparman, M., Woodward, J., Ramsey, C., Xu, J., Kang, E., Amato, P., Mair, G., Steinborn, R., & Mitalipov, S. (2012). Rapid Mitochondrial DNA Segregation in Primate Preimplantation Embryos Precedes Somatic and Germline Bottleneck Cell Reports, 1 (5), 506-515 DOI: 10.1016/j.celrep.2012.03.011









replacement of certain genes of the embryoa couple with a faulty set of mitochondrial genes to completely replace these genes from another donor looks at complete replacement of genes

Wednesday, April 30, 2014

Familial traits, disease risks and now, Faces!


Animation of the structure of a section of DNA...

How very often do we see forensic experts on TV, nab the killer using trace amounts of DNA that were found on the carpet or victim’s clothing? While these actors convincingly make the process seem very simple and quick, it is only the people who work in the area of forensics know how difficult and tedious the entire process is. The trick is not only in getting that little amount of blood/ saliva/ skin sample from the crime scene but also having a sturdy database of DNA markers such as CODIS to compare the results against. Without a database (which, not to forget, takes years of data gathering to make), even with bucket loads of DNA to test, a forensic expert would not be able to link the the suspect to the crime scene.

But what if we told you that one could now simply get a 3D sketch of the person whose DNA was found at the crime scene. Wouldn’t that make the job of forensic experts and the cops much easier. Well, recent study published under the guidance of Dr. Mark Shriver of the Penn State University can make this very much a possibility in the near future.

To do this, Dr. Shriver teamed up with a imaging specialist, Peter Claes, from the Department of Electrical Engineering, at the University of Leuven, Belgium. Using high resolution photographs, from almost 600 volunteers, they compared these faces against a face model that had over 7000 points of reference. With similarities and differences compared, the researchers were able to identify 44 principal components which could account for 98% of variations seen between faces.

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Face Model with over 7000 points of reference
Image source: doi:10.1371/journal.pgen.1004224.g001
While the imaging work was under way, Dr. Shriver used his expertise in population genetics to correlate the presence of polymorphisms in certain genes with the variations in facial features. After preliminary research, Dr. Shriver and his team began with a data set of 50 genes that were known to play a role in generating variations in facial shape. The researchers were already aware of the impact of sex and ancestry have on our facial development and after extensive testing of DNA obtained from the volunteers, they were able to identify 24 polymorphisms* that had significant impact on development of facial features.

Advances in the field of of population genetics now allow us to broadly classify the race of the person whose DNA is found at the crime scene. Thus, forensic experts are able to provide accurate information on whether the suspect, whose DNA is tested, is either African, European, South Asian or Native American in origin. Learning from the study, forensic experts will now be able to further test the sample for polymorphisms and use the data generated from these tests to create a 3D facial map of the person. While this might still be far away from its field application, this study has opened doors to a realm of possibilities in the field of forensics. Further research might also be able to reveal additional details such as hair colour, skin tone, other unique features that might help in identification of the culprit. We might not be far away from the future, where finding trace amounts of sample at the crime scene could simply give the cops a 3D ‘mugshot’ of the culprit.

Are you reading this, writers of sci-fi TV shows?

*- Polymorphisms -  mutations in our DNA that are quite common in population but do not cause disease




ResearchBlogging.org
Claes P, Liberton DK, Daniels K, Rosana KM, Quillen EE, Pearson LN, McEvoy B, Bauchet M, Zaidi AA, Yao W, Tang H, Barsh GS, Absher DM, Puts DA, Rocha J, Beleza S, Pereira RW, Baynam G, Suetens P, Vandermeulen D, Wagner JK, Boster JS, & Shriver MD (2014). Modeling 3D facial shape from DNA. PLoS genetics, 10 (3) PMID: 24651127
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Friday, April 18, 2014

Cloak of Invisibility very much a possibility!


Harry Potter’s invisibility cloak is one accessory every Muggle would like to include in their wardrobe. For those of you who are not familiar with Harry Porter terminology, Muggles is the term, magic folk use to call non magical folk (and invisibility cloak is self-explanatory). We Muggles may not possess magical powers to conjure an invisibility cloak, but we surely have technology and genius, to fashion ourselves one.

A simple principle exists behind the theory of invisibility. We can only see objects which reflect light incident on them, so in order to make any material or object invisible the reflection of light should be disabled. This is a simple concept but its execution is extremely difficult, and until now it was considered almost impossible. The phenomenon was reality with the use of artificially structured materials known as “metamaterials”.

Metamaterials are unique materials which defy the natural law of absorption of light by materials which are considered to be written stone. The light can only pass around this material, not through it. Now, how are these materials actually made? These materials are assembled from photonic crystals to wires and foam. These are then scaled at level smaller than the wavelength aimed for manipulation so as to force the light to bend around the material. The waves which are aimed at manipulation usually include microwave, infrared or visible light. To change the behaviour of this material scientists have realised that the shape of the material plays a major role besides the material itself. The metamaterials used to make a cloak of invisibility was observed to show images behind the cloak donner but the image was blurry and darkened. Scientists then realised that sharper edges did a better job of invisibility and hence by further experimentation they created a diamond cloak with the corners matching the required properties carefully.

Even though the little tweaks enhanced invisibility offered by this super impressive material this was not the end of obstacles. First obstacle was that this cloak worked only in one direction. The second was tuning it to match the required wavelengths. With further experiments if these issues are solved then we get one step closer to making our own Hogwarts here!


What would we use all this invisibility for? Other than fun stuff like playing pranks and hiding from your boss, this invention will play a vital role in military and telecommunication. Since invisibility can be the biggest asset for any army, metamaterial uniforms will find a place in the military. Other than this these metamaterials have the potential to join the wireless charging technology bandwagon. Several major industries have patents for these chargers and even though their working is kept under wraps, the usage of metamaterials has been emphasized abundantly. Besides these cool uses, the cloak of invisibility may also help in averting earthquakes and tsunamis. Even though this is a slightly more difficult goal to achieve, it is not impossible!

Further Reading
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