Discovering the Olinguito, in the museum [Video]

An Olinguito
Photo courtesy: 
The Olinguito was one of the Top Ten New Species of 2014 and is a mammal that is found in the misty mountains of Ecuador and Western Columbia. While this carnivorous mammal has been spotted multiple times before and even displayed in the zoos of the United States before, people mistook the creature for a common racoon.  However, olinguitos are tree-living animals and prefer to habitat stretches of mountains that are 5000-9000 feet high. They just have a single mammary gland and bear a single offspring at in a single gestation. 

It actually took an accidental discovery in the museum to get the classification right! Here is the story of the Discovery of Olinguito by Kristofer Helgen and how specimens are maintained and analysed in the museum courtesy of the Shelf Life series from the American Natural History Museum 

A Wall-E Future?

Set in the year 2805, WALL-E sent the world in a wave of "aweee"s as movie goers came out of the theatres overwhelmed with gestures of the cute little bot. While WALL-E (short for Waste Allocation Load Lifter -Earth class) was conceptualized to sort out wastes on planet Earth while its irresponsible future inhabitants cruised around the world, little are we realising that slowly and surely, we are moving towards a future, quite alike the movie, WALL-E. 

It is likely that our readers are thinking on the lines of how we are polluting our Earth and the rampant deforestation that accompanies the "development" of our civilization, but today we would like to talk about automation instead and how we are moving towards a future that includes having robots in our daily lives. 

Smartness is a quality no longer limited to phones and television sets but something that has moved further to devices. As we become used to the Internet of Things as it is developing around us, it is also time that we accept that robots will also become ubiquitous around us in the years to come. Rather, they will become so common that we might hardly notice them.

Take Google Cars for that matter. We are very open to the concept of driverless cars on the roads in a bid to reduce accidents, without realising that it is computer or a robot that will maneuver this vehicle. Yes, it is not the traditional Android bot that have been repeatedly enforced to think that robots are. Rather, this robot will sit inside the hood of your car, with its eyes on the roof and other sensors on the front and back, a navigation system that will let it decide its course and probably a voice modulated digital assistant that will communicate with you. While this seems like a massive accomplishment for artificial intelligence, similar systems (auto pilots) have been managing our aircrafts for decades  now.

Another robot that will soon become common sighting is the TUG from Aethon. Developed specially for hospitals, the TUG robots are designed to handle everything that a helping hand in a hospital would do. From taking medicines to different floors, to dropping off samples in the lab or even delivering food to patients on time the TUG can handle it all. The robots come in different specifications, designed to handle specific tasks but more or less look just the same. The TUG robots even do the dirty work like cleaning out the trash or taking dirty linen to the laundry with equal ease. All you need to do is tell them where to head and leave them free to do their work, absolutely no monitoring required.

All TUGs are controlled through the command stations where you can list the different tasks you want the TUG to do. Once programmed just hit the go button and TUG will be on its way. With sensors that function as its eyes, TUG can gauge if it is about to collide with a human or a non-human and quickly take evasive action. It knows all routes within the hospital and can even call the elevator to travel to another floor. What is more, when low on battery, the TUG finds the nearest charging station to recharge itself before moving ahead. So, you need not bother to find these TUGs lying around somewhere one day. There is no doubt that the University of California San Francisco Medical Center ordered 25 such TUG bots to help them with their day to day activities.

You can watch the TUG in action in the video below and do let us know if you think that we are not moving towards a WALL- E future! 

Aethon TUG Robot: Automating Internal Logictics from Aethon on Vimeo.

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Can we 3D print our organs?

Right from an actual firing gun to a camera lens, funky phone holders to even a musical flute, 3D printing has expanded our horizons of what can be made by with the help of a computer. But can we trust this technology to go beyond these everyday things and make something that can be truly life saving?

Well, there have been reports where 3D printing has helped doctors create a replica model of a faulty heart before attempting surgery on a two year old  or even help trauma patients rebuild their faces with 3D printed parts, but we would like to push these frontiers even further and get these printers to print something more amazing, more like a liver we could transplant or a heart that could pump blood for real. 

While this might sound like a technology stolen from the future, the fact is that there are companies working today towards making this possible and have even got as far as printing a particular tissue on demand. Organovo, a San Diego, California based company, actually takes orders for printing liver tissue so that drug companies can test their new drugs on them, before taking them for clinical trials. 

Usually, drug trials are carried out on cultured cells in the lab, before a clinical trial is attempted. However, sometimes the results of lab trials and clinical trials do not match and the reason for such a mismatch is the difference between the real and lab worlds. 

In the lab, cells are grown in a culture flask where they grow next to each other on a flat or 2D surface. However, in the real world, cells of a tissue or organ grow next to each other and even on top of each other, something we would call a 3D structure and here the dynamics of taking up a drug and processing it might change. 

Organovo's innovation is this regard is their ability to print tissues in 3D and then use for testing purposes. Here is a video explaining how the printing process works and how drugs can be tested. 

So far, the company has been able to make available its 3D printed liver tissue for trial purposes but is also working with others to create disease tissue for rare disorders so that potential drug targets can be tested with much greater accuracy.

With the progress report so far, printing organs for ourselves which can specifically match our requirements does seem to be an achievable feat in the near future, doesn't it?

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Behind the Scenes: The American Natural History Museum [Video]

Insect Samples at display in the Invertebrate Zoology Division at American Natural History Museum (AMNH). Photo credit: AMNH
Insect Samples at display in the Invertebrate Zoology Division at American Natural History Museum (AMNH).
Photo credit: AMNH

If you have ever marvelled at how a museum is curated, its collections maintained and who are the people who create the magic therein, then here is your chance to find out more about the happenings inside, sitting in the comfort of your home. The American Museum of Natural History at Central Park West, New York has recently started a video series called Shelf Life on YouTube, which takes us behind the scenes of the popular museum.

The first Episode premiered in November last year and is titled 33 Million Things, an approximate number of artifacts and specimens that the museum holds and gives a sneak preview of what we can expect from the year long series. From Zoological specimens to terra bytes of images of stars, galaxies and planets, frozen DNA and tissue samples and artifacts from Native North American culture, the series opens doors to this huge ocean of information that is the American Museum of Natural History. And in case you have any doubts, museum scientists and collection staff will guide you along the way.

So, without further ado, here is the first episode of the Shelf Life! If you like it, do Subscribe to the AMNH Channel on YouTube  or simply Subscribe to our blog and we will bring you all the updates!

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. 

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