RotM: Interview with Dr. Allan Drummond

Dr. D. Allan Drummond. Photo Credit: Dr. Allan Drummond
Dr. D. Allan Drummond in his office at the University of Chicago
This month, we spoke to Dr. D. Allan Drummond, our Researcher of the Month (RotM), regarding his work about proteins. Dr. Allan has a Ph.D in Computation and Neural Systems and heads a team of scientists as Assistant Professor of Biochemistry and Molecular Biology as well as the Department of Human Genetics, University of Chicago. His team works on finding out the effects of errors in protein making mechanism in our cells and their effect in disorders such as Amyotrophic Lateral Sclerosis (ALS)

In this interview, Dr. Allan simplified for us his recent findings about tRNA modification that were recently published in PLoS Biology 

CTS: What is the aim of studying tRNA modification? What information can we seek from studying tRNAs?

AD: We study tRNAs and their modifications to understand translation, a fundamental biological process shared by all life. Cells need proteins, the main molecular workers in biology. To make proteins, ribosomes in the cell translate the genetic information in messenger RNA using tRNAs. Modifications to tRNAs potentially change how translation works, with all sorts of consequences (to cellular health, and even to the evolution of genomes) so we’re interested in understanding that.

English: Codon-anticodon pairing exemplified f...
English: Codon-anticodon pairing exemplified for a tRNA Ala (Photo credit: Wikipedia)
To draw an analogy, consider another fundamental biological process: digesting food! You eat food and your body turns it into all sorts of things by digestion. So what happens when you chemically modify your food, for example by cooking it? How does cooking change digestion? Is it easier or harder to digest cooked food? Does digestion work more or less efficiently on this modified food? These are really basic questions, and because the process is so important, it just feels like getting in there and studying it is likely to yield important insights. That’s one of the things that drove us: raw curiosity about how chemical modifications change a basic biological process, in this case tRNAs and translation.

tRNAs are interesting because they physically embody the genetic code that maps triplet codons to amino acids. tRNAs have a triplet anticodon on one end (like ‘GUU’) that recognizes the triplet codon in mRNA (like ‘AAC’), and at their other end, they’re charged with an amino acid which, most of the time, corresponds to the codon (in this case, asparagine).

I say “most of the time” because ribosomes make mistakes, sometimes allowing a tRNA to recognize a different codon than the one it’s supposed to. In our study, we’re interested in the errors that ribosomes make as they translate.

CTS: How has this study contributed to existing scientific knowledge?

This image shows a 0.1 x 0.03 inch (2.5 x 0.8 ...
Drosophila melanogaster, fruit-fly.
(Photo credit: Wikipedia)
AD: At the most basic level, our study reveals a surprising and new way in which nutrient availability alters the evolution of whole genomes. To reach this conclusion, we stack up a set of results, one on top of the other. We discover big changes in the way animals (fruit flies) within a genus encode their proteins in their genomes (which codons they use), and show that these changes reflect the relative accuracy with which alternative codons for the same amino acid are translated. 

Making the educated guess, based on our own study and previous work, that a tRNA modification is involved, we measure the tRNA modification levels for multiple species, and find that these levels change systematically. Then we show how just these modification level changes can be sufficient to explain the change in translational accuracy and genome changes. And we make a prediction, which the data support, that the changes in tRNA modification levels as flies develop from eggs into larva into pupae into adults should correspond with changes in the codons used in genes that are turned on during each developmental stage.

CTS: How was translational accuracy tested before Akashi's method was introduced?

AD: Not very cleanly! Akashi’s work was really a remarkable advance. Some papers had made hypotheses about how selection on translational accuracy should work, and tested those hypotheses. For example, you might guess that the more amino acids in a protein (the longer it is), the more likely an error is to occur before translation is complete, so there should be stronger selection to prevent errors in long proteins. The problem, here, is that long proteins and short proteins differ in all kinds of other ways: they can be produced at different levels in the cell, have different functions, and so on. What Akashi did was come up with a way to test for differences within a protein, by comparing certain codons to other codons in the same sequence. His method naturally controls for all these other differences, so it really was a profound advance. I’ve been using his method, or variations on it, for many years, and feel it’s one of the most satisfying methods developed in the study of molecular evolution. That’s one of the reasons we named our modified measure the “Akashi selection score,” to do a bit more than just credit his work.

CTS: You have mentioned that queuosine modification is dependent on the intake of queuine, which is again obtained from bacteria.  Isn't there is back up mechanism for this? What happens if queuine is not available for some reasons?

AD: Short answer: we don’t know!

At many points in the paper, we remind the reader that while queuine is not made by eukaryotes, it doesn’t necessarily need to be obtained by eating. Animal guts are filled with bacteria--the gut microbiome--and these bacteria are constantly growing, dying, and shedding their contents into the gut, where they can be absorbed by the host. So it may be extremely difficult to deprive animals of queuine!

In the lab, it’s possible, however. In studies where animals have been entirely deprived of queuine/queuosine, by raising them in the absence of bacteria, the animals do pretty well, at least in the short term. That lack of a clear phenotype is one of the main reasons queuosine’s function remains unclear. Provide biologists with a clear phenotype, and they’ll go berserk until they’ve figured out what causes that phenotype. No clear phenotype = sad biologists = much slower progress.

That lack of a dramatic phenotype could be because queuosine modification make a big difference, but under conditions we haven’t checked yet, like starvation or severe stress or when being chased by large predators or by amorous potential mates.

Lack of a phenotype could also be just lack of human-measurable phenotype. Natural selection can see tiny differences that humans can’t. For example, if flies deprived of queuine (say, due to a mutation that prevents queuine absorption) produce 0.01% fewer offspring on average than wild-type (“normal”) flies, we’d never know; they look the same to us humans and our tools. It’s like being 0.01mm taller than your brother -- might be true, but whose ruler would you use? But in the wild, standard models tell us that queuine-deprived mutant fruit fly and its descendants would quite efficiently go extinct over evolutionary time, outcompeted by the wild-type flies. So seeing “nothing” in the lab does not mean there’s no biologically (= evolutionarily) important effect. That queuosine modification of tRNA is maintained in almost all eukaryotes indicates that there are, indeed, evolutionarily important effects. We’ve just got to find them.

And that’s the long answer to “what happens if queuine is not available”? Maybe something, maybe nothing in the short term, but maybe something that just looks like nothing given our scientific limitations.

CTS: We do not quite know the detailed role of queuosine in tRNA translation. How could we do that? Is your lab working this aspect too?

AD: You’re right. One of us (Tao Pan) is a hard-core RNA biologist who’s made a career out of studying tRNA, RNA modifications, and translational fidelity, so you can bet we’re going deeper. The deep mechanistic aspects of how queuosine alters translation will likely need to wait for the ribosome jockeys to get interested. And that’s one of my hopes, that our paper helps spur interest and new studies from other groups. I think it’s remarkable to see such a set of interlocking questions, spanning diet, the microbiome, speciation, translation, and genome evolution. There’s plenty of work to be done!

CTS: Moving away from the paper, in your personal opinion, do you think that other studies such as those involving cancer, Alzheimers etc. get more media attention , whereas fundamental studies do not?

AD: That’s an empirical question, not a matter of opinion. I think, of studies receiving media attention, more of them do tend to be focused on cancer and Alzheimer’s disease than basic science, but I also think that’s not quite what you’re asking.

The question I sense you’re asking is, should cancer/disease studies garner more media attention than fundamental studies? Or, does it bother me if the media doesn’t seize on what we’ve found and broadcast it to the world?

Short answer: not really. Broad media attention is not the goal, and doesn’t really help us or the science.

Media attention tends to follow studies that appeal to the consumers of those media. The Financial Times has few readers who would, or should, care about our results. The impact of what we’ve done on those readers’ lives for the next several years is probably zero.

However, other media channels exist. Publishing this work was my first experience sending a relatively high-profile paper into the social media world. It got plenty of attention, more than I ever expected! Most of this attention was on Twitter, from scientists sharing it amongst themselves. And that’s great, in my view; attention is just awareness at this stage, and serves primarily to ensure that people read and scrutinize what we’ve done, pull out the gems, locate the flaws, maybe even change the way they think about their research.

As a basic scientist, I crave attention 10-20 years from now. The dream paper, for me, is one that becomes an indispensable part of human knowledge because it turns out to be a pivotal insight, an influential line of thought spawning a whole field of inquiry, a robust result that holds up in the face of scrutiny, a useful advance. At this stage in science, I don’t think we can predict those features (pivotal-ness, influence, robustness, utility) when the paper comes out. Media attention for anything other than entertainment value is premature. We have to let the clock run and see what happens.

That said, I do love the idea that there’s a person out there -- a flight attendant for Lufthansa, say, or a human resources manager for a software firm in Bangalore -- who stumbles on our paper, downloads it (open access!), and sits there, on their break, pushing through the thickets of jargon and unfamiliar abbreviations, and grasps the outline of what we’ve done and what it might mean, and smiles in a way they haven’t ever. 


Reference: 
Zaborske JM, DuMont VL, Wallace EW, Pan T, Aquadro CF, & Drummond DA (2014). A nutrient-driven tRNA modification alters translational fidelity and genome-wide protein coding across an animal genus. PLoS biology, 12 (12) PMID: 25489848

10 lesser known facts about Lightning


Lightning over water Photo credit:www.nationalgeographic.com
From the Greeks to the Norse and Shinto to the Hindu mythology, lightning has been a sign of wrath in almost all cultures. Both feared and revered, lightning is the symbol of power and authority and even the famous Harry Potter carries this symbol on his forehead. While the clap of thunder that accompanies lightning can startle anybody easily, one cannot undermine the spookiness that a bolt of lightning can bring to a dark night with some strong winds blowing. Whether we speak of stories of mythology or a scary movie, lightning manages to add its own dimension every time. 


Here’s adding a little more to your know how about lightning.

  1. Carrying almost 300KV of energy, a spark of lightning can raise the temperature of air to about 50,000 Fahrenheit, that’s about 27,700 degree Celsius. The surface of the Sun is around 5500 degrees Celsius. So, with every bolt of lightning, we, temporarily, have the temperature of 5 Suns striking the Earth. Luckily, these high temperatures stay for just a few milli-seconds and not long enough to burn up the Earth. However, these high energy shots coming from the sky are sufficient to light a tree of fire instantly and are the starting points of many a forest fires and the destruction that follows after.

2.  ‘Lightning does not strike the same place twice’ is just a myth.  Rather the opposite seems to be true, especially for tall, pointed, isolated structures. The famous  Empire State Building in New York City is hit nearly 100 times a year and there are many photos of this sight that you will find on the internet.

If you are living in a tall rise, there is no need to panic though, since such buildings are equipped with lightning conductors that allow lightning to pass straight to the ground with harming the residents. Never the less, if you are out in the open, do not try to tempt fate by occupying the spot that has just been hit by lightning.

 3.   If conditions are right, and all the necessary ingredients (like silica or quartz) present, lightning
Fulgurite
can fuse silica to form glass. These amazing structures are called Fulgurites and are incredibly beautiful and delicate, with thin glass tubular interiors covered with sand outside, generally found in the branched out shape as lightning itself.  You can own a piece of this natural beauty by paying Science Mall USA a sum close of $300 or if you have some budgetary concerns, you can also choose a fulgurite pendant or ear-rings for around $100. Hunting one such structure down should also not be very difficult, for you can find lots of educational websites speaking about where to find Fulgurites.



Lichtenberg figure. Image credit: www.teslamania.delete.org
4.  The fascinating shape of the lightning bolt running through an insulating material is called a Lichtenberg figure. This figure, was first discovered by German physicist Georg Lichtenberg in 1777, when he was attempting to learn about the nature of positive and negative electric fields of lightning. Little did Mr. Lichtenberg know that he was laying the foundation for modern day plasma physics.

These figures are quite popular for the fractal pattern that they leave behind. If you are looking for more information on you can find it here.   

But insulating materials are not the only one to get these Lichtenberg figures. People who have been hit by lightning and survived to tell the tale also carry these fascinating shapes on their body. Called, ‘lightning flowers’, these shapes are likely to be caused due to capillary rupture beneath the skin but are definitely a horrid reminder of what the person has gone through.

5. Although lightening forms some cool patterns and, fictionally speaking, may even bestow supernatural abilities in people it strikes, in reality, it is often life threatening. With temperatures that are 5 times as much as the surface of the Sun, a direct lightning strike can leave a person charred, boiled and very very dead. More often people who get struck die instantaneously of a cardiac arrest. And if they do survive, they live with irreparable neurological and psychological damage. A study found out that many patients of lightning injury suffer from motor paralysis of upper extremities which can take a few days to recover. However, psychological effects such as hyperirritability, high levels of anxiety, attention deficit and post traumaticstress disorder remain with these patients for extended periods of time.

6.   While old Japanese folklore has spoken about how mushrooms seem to surprisingly grow well
Mushrooms Image credit: www.bascianifoods.com
during a thunder storm, it took modern day research to finally say that this may be in fact true. A single bolt of lightning is known to be fatal and can easily char the fungi or even a complete human being, but a weakened charge that travels through the ground can result in an increase in mushroom production.

Scientists are working to come up with technology that will allow farmers to simulate this artificial lightning. Similar experiments done with radishes have also borne similar results and so a small bolt of electricity seems to be doing the trick for the farmers.  So, if you have been thinking about having a bountiful mushroom crop, think about charging up a few things around and see how well the mushrooms grow.

7.  A Superbolt is a powerful and unusually bright lightning bolt. These occur once in every million lightning strikes on Earth but are said to be very common on Jupiter. Yes, lightning does occur on other planets as well and there is evidence to support that lightning has been seen on Venus and Saturn as well.  Lightning on another planet is an interesting piece of information for scientists, since the energy is lightning can be the causative factor that can break compounds or fuse them together in surprising ways, some of which might also be responsible for supporting life.

An interesting bit of information about lightning on Venus is that it originates in clouds that are made up of sulphuric acid. Definitely something to remember for the future, when we manage to put up a few people on the planet and start colonising it.

8.   If you are not bothered by lightning that strikes outdoors while you sit comfortably inside your room and read this post, there is something that you should really know. People have been struck by lightning indoors as well. How you ask? Well, these were people who managed to touch a good conductor while it was lightning outside. Plumbing pipes or telephone wires that occupy most walls of a building and are more than happy to carry the bolt of lightning with them and although your room might seem like a safe place to hide, it can actually be a mesh of electricity within which you are sitting insulated. So, do stay away from all sorts of metal when its lightning outside.

9.  Lightning helps transferring genes into the cell.  Well, this is not something that you can take quite literally, in your case, since lightning will only leave you charred and not the recipient of some mutant genes but in case of bacteria, this is quite the truth.  Scientists are able to transfer new genes to bacteria (called transformation) by giving them a small electric shock in the lab.

While this is one of the methods of creating transformants (transformed cells) that researchers use in labs on an everyday basis, a study published in 2001 showed that this occurs naturally too and bacteria can get transformed due to lightning discharges in the soil. Just like, we mentioned that lightning can create or destroy compounds in the environment, this study has shown that lightning might have also aided the evolution of bacteria along the way.

10.   Harvesting the energy from Lightning:

A single bolt of lightning carries approximately 5 billion joules of power, which is sufficient to power a regular household for about a month. Our Earth receives about 1.5 million flashes of lightning every day. This translates to somewhere around a quadrillion joules of power available on an everyday basis, if we manage to capture it all. While this might be technically unfeasible at this point in time, it does offer to potentially be a plentiful resource of energy for one and all.

Some labs have every tried to charge a smartphone using simulated lightning and found that its batteries charge up in a matter of seconds. We can only wonder how quick charging electric cars can be and how revolutionary the technique will be in helping us rid our dependence on fossil fuels.

Alternate Energy Holdings Inc. (AEHI), is testing a method to capture energy from lightning and introduce it for everyday use. However, before this can be commercially feasible, we need a more reliable model to predict where lightning is likely to hit so that we can set up some kind of lightning capture farms.

Back after a break!!!!

Break: Image credit: www.wpclipart.com
To our dear readers who have been patiently looking at this blog for updates, our sincerest apologies!

We had to take an unplanned long break (nothing to worry about) but now we are back, and you can look forward to our upcoming posts!





A sneak preview at what you can expect in the coming few days!


  • Interesting bits about lightning? 
  • How to make periodical table more interesting! and
  • Our Researcher of the Month interview! 


Salt and Water Waltz [Video]


If you have enjoyed watching the video above, then you are going to absolutely love the science behind it that makes it possible! 

All this chemical dancing was made possible by a simple finding that we can move objects using sound waves. This requires no spells that you can learn only at the Hogwarts School of Wizardry, but just the simple application of acoustic levitation. Scientists have been able to levitate light objects using nothing but sound waves (at particular frequencies) from a speaker. But researchers Dimos Poulikakos and Daniele Foresti at the University ETH Zurich have modified this well known method that not only allows them to levitate objects but also move them to their hearts desire! The result, the salt and water waltz above. 

This technique is known as acoustophoresis in the scientific world and can be applied in the pharmaceutical industry where one wishes to mix ingredients without contaminating them. 




If you work in a lab that has contamination issues, this is a sure shot way of avoiding it. A suggestion worthy of taking to your next lab meeting, we say! If you have liked reading this post, why not follow our blog, using the Subscribe button on the screen or following us on your favourite social media, whether it is Facebook or Twitter or Google+) and making a resolve to read every post that we send your way. 



What is Shrimpoluminescence?

Pistol shrimp : Image source: ParadisePetShop.net
It is likely that you have heard the terms Chemiluminescence or Bioluminescence. While the former is light created during chemical reactions, the latter is the light created by living beings such as glow worms and plankton. But have you come across the term 'Shrimpoluminescence'?. Well, if you have not, welcome to Coffee Table Science, where we tell you today what is Shrimpoluminescence

Before we get there, you must first understand what sonoluminescence is. It is light created in a liquid by imploding bubbles, when they are excited by sound waves.

Scientists Frenzel and Schultes at the University of Cologne accidently came across this phenomenon when they were hoping to quicken the development process of photographic films by using ultrasound frequencies. Since, the scientists were working with developer fluid, they noticed tiny dots on the photographic film once it was developed. But it took a wait of another 55 years before Philip Gaitan and Lawrence Crum could design an systematic experiment where the phenomenon could be studied properly. 

When a bubble inside a liquid is struck by a sound wave , it implodes at a rapid speed which causes the air molecules inside the bubble to collide against each other, which generates heat as well as light. What we know so far is that the temperature inside the imploding air bubble is close to a 5000K i.e. the temperature on the surface of the Sun but the whole event wraps up in matter of few hundred picoseconds ( 10 to the power minus 12th of a second). Below is a short video to show you how exactly this happens. 




It has been noted that inert gases such as argon, neon etc. are much better at emitting light in this fashion and experiments have been modified further to even get the bubble to rapidly implode and reach back its original state thereby gaining a continuous light emission from this set up. While the light is only a by product here, the interest in sonoluminescence is due to the fact the core temperature of the bubble has the potential to reach 20,000 K and probably one day we will manage a method to harvest it and utilize it for our benefit.

So far, what we have managed though, is controlling the phenomenon in a way where we can see this light being emitted continuously, something that Professor Seth Putterman, calls

A Star in a Jar



So, heading back to where we started, pistol shrimps use a very similar mechanism to hunt down their prey. By using their claws, these shrimps create small air bubbles that they can shoot. The bubble shot by the shrimp hits the target at a speed of close to 100 kmph, which is good enough to kill it instantly or at least stun it, in case, its a big fish.

While the light produced in this method is invisible to the naked eye, the mechanism is quite the same and therefore, when the phenomenon was discovered in 2001 by Michel Versluis and his team at the University of Twente, Netherlands, they called it, Shrimpoluminescence. 




If you have liked reading this post, why not follow our blog, using the Follow Button on the screen or following us on your favourite social media, whether it is Facebook or Twitter or Google+) and making a resolve to read every post that we send your way. 

Plus, there is another interesting post about Leidenfrost effect on our blog! Happy reading! 

Science and Christmas [Video]

When it comes to Christmas and Santa Claus there are so many questions that we don't seem to have answers to. Being a skeptic can sometimes take the fun out of the whole festival. 

Well the guys at AUT University (Aukland University of Technology) have tried to answer a few of those baffling questions, so that we (the skeptic) can lay back and enjoy the very things that make Christmas the greatest time of the year.


Burn some rocket fuel in your house! [Video]

If NASA and ISRO are sending rockets successfully into space every now and then and you are feeling a little bit left out, you can burn a little bit of rocket fuel yourself, using some packet pasta and dry yeast.



 Although this will not take you very far, it is definitely going to be be a lot of fun! 

You never travel Alone!

Travelling alone. Image credit. www.redcranetravel.com
If you are quite the traveller who likes visiting different countries and posting Instagram pictures of historic sites and tourist places you have been to, this is the probably the right time to tell you this

'YOU ARE NOT TRAVELLING ALONE'

Well, this is not about some stalker following you or the government that keeps an eye on each and every one of us. Instead, this is about the unknown baggage you are carrying with you while you are criss crossing continents in the comfort of an aircraft, viz., the many many bacteria and fungal spores and the microscopic creatures such as house mites.

The Finding 

In a recent study published by researcher Rubaba Hamid Shafique and her colleagues from the Pir Mehr Ali Shah Arid Agricultural University in Rawalpindi, Pakistan and University of Michigan, USA, the researchers studied two house mite populations from these two countries. On sequencing small parts of their genome, the researchers found these organisms had quite a few things that were common in their genome sequences. 

The Explanation 

House dust mite (Dermatophagoides pteronyssinu...
House dust mite (Dermatophagoides pteronyssinus)
(Photo credit: Wikipedia)
Ideally speaking sequencing should reveal that the sequence of nucleotide bases (building block of genome) for a specific region are the same. This is especially true if one is sequencing conserved regions of the genome, which are basically regions of the genome that code for proteins that are common across organisms. (This is another proof that we have all come from a common ancestor, something that could be discussed in another post on another day). 

What Rubaba Hamid and her colleagues found was that not only did these organisms had matching sequences, they even had matching mutations. Now, mutations in a population are random events. So, if a house mite population develops a mutation at say nucleotide position 10, then the chance that another house mite population in the United States at the same nucleotide position in extremely rare. However, what the study goes to say is that the author found such mutations in not one not two but 14 spots in the small bit of genome that she was looking at. Not only this, the sequence and the mutations therein found for house mite populations in Pakistan, exactly matched those that were reported in house mite populations in Thailand and China. 

Such similarities in the genome can occur, if and only if, house mite population from these countries have met each other before and mated to produce offsprings that carry their mutations. Since house mites are not capable of finding love internationally all by themselves, the authors say that it is obvious that are piggy backing our back packs as we travel. While these little beings are happy to hide in the sofas and mattresses for most part of their lives, a few of them are adventurous enough to make that extra effort to get into our travel clothes and end up in another country without any visa. Knowingly or unknowingly, these mites are capable of using man made technologies for their own benefit, progress and spreading themselves out in the world. 

Although it might seem a trivial thing at the outset, the issue of travelling microbes is quite serious and a major impediment in the global health care scenario. The recent scare of Ebola and its rapid spread over many nations is primarily due to the rapid means of transport available today and the frequency with which people travel for business or pleasure. 

So, the next time you take a flight to Hawaii or Switzerland for a vacation, do give a thought to what might be carrying from back and what you might be bringing back. 

Reference: 

Shafique RH, Klimov PB, Inam M, Chaudhary FR, & OConnor BM (2014). Group 1 Allergen Genes in Two Species of House Dust Mites, Dermatophagoides farinae and D. pteronyssinus (Acari: Pyroglyphidae): Direct Sequencing, Characterization and Polymorphism. PloS one, 9 (12) PMID: 25494056