Science Simplified!

Thursday, October 30, 2014

When Rocket Science Fails [Coffee-byte]

2:42 PM Posted by Editor CTS , , , No comments
Image source:
www.gizmodo.com
Even with all the developments in space technology and successful missions being sent to Mars, there is always a chance for something to go wrong. The Antares Rocket that supposed to carry supplies and science experiments to the International Space Station, exploded six seconds after take off from the Wallops Flight Faclity in Virginia. 

Although no one was injured, the loss of cargo and devastation at the launchpad would run into millions of dollars for NASA. The real estimate of loss will only be known after a complete analysis is done. The rocket, ferrying cargo to the ISS, was developed and operated by Orbital Sciences Corporation, which has already delivered cargo twice to the ISS. NASA has confirmed that there was no critical cargo on the flight and supplies on the ISS will not be affected by the failure of the mission. 

But irrespective of the losses, the failure of the rocket launch teaches us one important thing about space research, that there is a lot more to learn!

Sunday, October 26, 2014

Transplanting a dead heart is now possible! [Coffee-byte]

Heart Transplant
Image source: www.thehealthsite.com 
In a ground breaking discovery in organ transplantation, doctors in Australia have been successful in transplanting a heart that had stopped beating for about 20 minutes. Usually, hearts are received from donors who have been declared brain dead but whose hearts are still beating. In this case, the heart had stopped beating but was then revived and then transplanted into a patient suffering from congenital heart failure. This transplantation was conducted at St. Vincent's Hospital in Sydney with the help of an innovative new device called OCS Heart.

The biggest constraint for heart transplants is that beating hearts can be kept on ice for only up to 4 hours within which they need to be transported and transplanted. This constraint majorly reduces the radius within which a heart can be transplanted to a needy donor. In addition to this, there is also a risk that cold conditions used during transportation may alter the activity of the heart which can be detected only after the heart has been transplanted.

The OCS Heart,on the other hand, maintains the heart is a warm environment where it continues to beat and is constantly monitored for its activity. Developed by TransMedics, OCS Heart provides an opportunity to store the Heart in working conditions for longer time duration, which will not only allow for it to be transported to larger distances but also give surgeons an opportunity to assess the organ before being transplanted. You can see the working of the instrument in the video below. 



The OCS stands for Organ Care System, which basically means that similar technology can be adopted for transporting other organs such as lungs and liver. TransMedics is also conducting clinical trials for these organs and is hopeful of commercially making this technology available soon.

Thursday, October 16, 2014

Under the MRI

9:00 AM Posted by Geetanjali Raikar , , No comments


Image courtesy: Andy Ellison (http://insideinsides.blogspot.in/)

The MRI or the magnetic resonance imaging technique is probably one of the best modern day scientific inventions. this non invasive procedure has allowed us to peer into the human body and enhanced our understanding of ourselves. 

After my recent post on Sex under the MRI and the fascinating images the machine produced, I got to fishing outs some other fun stuff captured by this incredible machine.  Here's what I found! 




1. Woman giving birth
 The video captures what happens inside the womb, just moments before the baby's birth. 





2. Unborn twins 

This video is really fascinating. This is probably the clearest visual of what is happening inside the belly.


3. Fruits and Vegs

Captured by Andy Ellison, these images are a result of mere curiosity and fascination of how fruits, vegetables and flowers look under the MRI. I stumbled upon these images at petapixel.com, and the internet hound that I am, I sniffed my way to Andy's homepage, and I was absolutely blown away. Here are a few images of what I saw but I highly recommend you go and check them out for yourself. (Dont forget to check out his older posts.)















Answers- Banana, Maize/Corn,Garlic, Brussels Sprout, Cucumber, Tomato , Sunflower, Banana Flower, Onion, Grapes.

Image in the beginning - Broccoli 

Wednesday, October 15, 2014

Space weather today! Chances of a solar storm?


Mars Mission, Rosetta, International Space Station and the myriad number of man made satellites orbiting the planet, have already made it obvious that the human race has reached an age where it is looking further beyond its home, the Earth. And now, with companies like Virgin Galactic closer to offering sub orbital space trips to one and all (who can afford it), it has become paramount that we look at the weather outside our Earth before embarking on a journey beyond our clouds. But what is space weather like ? 

We do know that outer space is a cold cold space and lacks any air. Astronauts head out for space walks in protective suits and a sufficient supply of oxygen, just the way we all saw in the movie Gravity. But it is not just the temperature and lack of air that we need to worry about, it is solar and magnetic activity in outer space that can impact us. 

What is Space weather

Space weather studies the impact of solar radiation and other high energy particles from outer space on the Earth's magnetic field and tries to predict the effect it has on conditions on Earth. The result of of the interaction could be minimal resulting in temporary increase of the Earth's magnetic field or colossal such damages to satellites orbiting around the planet. 

Did this begin recently? 

Space weather events are nothing new and have been occurring regularly for many many years. It is just that the human presence in near outer space has increased tremendously in recent years and so has our dependence on technology. Extreme space weather events can have damaging effects on electronic equipment that we have put out in space and this can impact our day to day lives. 

Impact of Space weather


       1. Damage to GPS

The most direct impact of an adverse space weather event would probably affect the Global Positioning System or GPS. The GPS works courtesy of the  24 minisatellites that cover the entire Earth (the principle has been simplified in this post by Melissa on AllSlate ). If an exodus of solar radiation brings down two or three satellites, we would lose our coverage over that area leaving users clueless in their locations, whether they are on land, water or in the air. 

     2. Loss of Radio Communication

While telecommunication might be booming around the globe, we still rely on radio communication for a large number of our day to day activities. All aircrafts correspond with Air Traffic Control centres using Hi-Frequency (HF) radio communication and an increased energy activity can result in blackout of this communication method. 

    3.  Power blackouts

Increased solar activity has the potential to rapidly vary the Earth's magnetic field as well. Varying magnetic field of the earth can then result in creation of an electric field that will impact voltage stability in high tension electricity transmission cables and transformers. In extreme cases, these fluctuations can cause blackouts for hours like the way the city of Malmoe in Sweden suffered in 2003. 

Not only will these disruptions affect day to day lives, correcting these disruptions requires a fair amount of time, effort and money to be spent as well. While replacing a failed transformer might take a few man hours, replacing a satellite requires millions of dollars of funding and months of planning and timely execution. 


How can we avoid this? 

Unfortunately, there is very little we know about solar activities and their occurrence rates to shield ourselves from its impact. There are only two things that we can do. 

a. Make robust devices and more of them. 

We need to figure out ways to make the instruments and satellites that we send up in space more robust so that they can withstand such events. The other thing to do would be make more of them. The GPS system actually has 27 satellites that are orbiting the Earth, so in case, some fail, the other can take their place. Similarly, the Russians also have a similar Navigational System in place called GLONASS (supported by most smartphones), which will serve as a back up for users of GPS till the services can be restored. 

b. Study Solar activity

We need to understand our Sun in a much better fashion and with this very aim the Met Office in the UK recently opened its Space Weather Operations Center in Exeter. Along with the Space Weather Prediction Center in Colorado, US, the Space Weather Operations Center will forecast the Space Weather for all of us. Why not check the latest Space Weather Prediction now! 





Friday, October 10, 2014

Tackling Ebola, once and for all.

9:00 PM Posted by Editor CTS , , , , , No comments
English: Transmission Electron Micrograph of t...
Transmission Electron Micrograph of the Ebola Virus. Hemorrhagic Fever, RNA Virus. (Photo credit: Wikipedia)
The epidemic of Ebola virus that began in December of 2013 has already claimed lives of over 2000 people, mostly in the West African region, where the outbreak occurred. The recent death of a Liberian citizen who travelled to the United States, probably after contracting an infection in his home country has raised further fears of how quickly the virus is being transmitted and is able to increase its reach. 

To make matters worse, there is no drug that is 100% effective against the virus and the few drugs that have been given limited clearances such as Zmapp and Brincidofovir are either out of stock or not available in enough numbers to contain the spread. The only means of containing the infection right now are preventing its further spread by following stringent protocols of containment and screening travellers who are flying out of affected countries and quarantining them on arrival. 

As other pharmaceutical companies test their potential drugs in clinical trials, stocks of partially effective drugs are expected to be restored and containment of the disease will become easier. However, this is just one type of Ebola virus that we have encountered so far and there are at least four other types in this family that are equally infectious and disruptive. Therefore, along with drugs, we need vaccines that will give us immunity against these viruses, something that also being looked into. 

But researchers at the University of Utah have identified the functionally critical region of Ebola virus, which when targeted with drugs will lead to more effective treatment of the disease. What makes this finding interesting is that this critical region is found in not only the Zaire Virus (responsible for current epidemic) but also seen in other Ebola viruses, making it an excellent candidate as a drug target. This will not only help us tackle this epidemic of Ebola, but also prepare us for any incident involving Ebola Viruses even in the future. 

Luckily, the critical region can be targeted with a class of drugs called D-peptides. These D-peptides are inexpensive to manufacture and also not digested by enzymes in the body, making them even more effective. Similar D-peptides are also being developed for HIV and will soon enter clinical studies. 


Reference:
Clinton TR, Weinstock MT, Jacobsen MT, Szabo-Fresnais N, Pandya MJ, Whitby FG, Herbert AS, Prugar LI, McKinnon R, Hill CP, Welch BD, Dye JM, Eckert DM, & Kay MS (2014). Design and characterization of ebolavirus GP prehairpin intermediate mimics as drug targets. Protein science : a publication of the Protein Society PMID: 25287718

Thursday, October 9, 2014

RotM: Interview with Prof. Kenro Kusumi

Kenro Kusumi with Jeanne Wilson-Rawls and Elizabeth Hutchins
Prof. Kenro Kusumi (R) with authors of the paper,
Jeanne Wilson-Rawls (L) and Elizabeth Hutchins (centre).
Photo credit: Joel Robertson. 
We, continue our Researcher of the Month initiative, with an interview with Professor Kenro Kusumi, who studies development, regeneration and diseases of the spine in his lab at the School of Life Sciences at the Arizona State University. Prof. Kusumi's expertise lies in developmental biology, embryology, evolution and genomics and recently published a paper in PLOS ONE on his findings from tail regeneration seen in green anole lizards which will pave way to finding regenerative treatment methods for diseases such as arthritis, scoliosis etc. 

CTS: For the benefit of our readers, could you please summarize your recent findings.

KK: In order to examine the genes that are differentially expressed within the regenerating lizard tail, we used RNA-Seq to assess all the genes expressed at 25 days of regeneration. This is a stage that marks maximal growth of the lizard tail, with formation of new tissues towards the base and patterning of those tissues towards the tip. We were able to read all the output of the 23,000 or so lizard genes in five sections along the tail in multiple replicates (n=5). By carrying out bioinformatic analysis and statistical tests, we found that at least 326 genes were turned on in specific spots within the regenerating tail. This gave us the first clues in the lizard as to the genetic ‘recipe’ for regeneration, and where each of the ingredients has to be used.

CTS: How do you envisage that your findings will be applied to treating patients in the future. 

Kenro Kusumi collecting specimen of anole lizards in Panama with Jeanne Wilson-Rawls
Prof. Kusumi with Prof. Jeanne collecting 
specimens of anole lizards in Panama
(Photo courtesy: Kenro Kusumi)
KK: Regenerating major parts of the human body parts will a challenge for the future. This research points out some of the avenues towards that goal. As anyone who suffers from arthritis knows, an important part of the limb are joints, which are cushioned by a specific type of cartilage. Lizards grow lots of this cartilage in their regenerated tails, and we hope to that this process can be activated to repair arthritis in humans. Lizards also regrow their spinal cord and their ability to use their tails. Activating nerve regeneration could help people suffering from spinal cord injury and would be necessary to regrow limbs.

Because lizards and people have a relatively recent common ancestor, compared with frogs and fish, we share many more similarities in the genome, or the genetic instructions within each cell. Almost all of the 326 genes that we identified in the regeneration are shared between lizards and humans. Over time, we suspect that these genes have changed between lizards and humans as to where and how much they are expressed in the tissue after injury. There are already drugs developed that alter the expression of some of these families of genes, and our hope is that in the future, we can reprogram cells for regenerative therapies.

CTS: Since we have a fair idea of how regeneration works and like you mentioned, even have a few drugs that can alter expression of certain genes, how soon would you reckon, that regenerative medicine will become part of mainstream treatments? 


KK:This is a hard question to answer, since clinical trials can be very time-consuming and slow. I would hope that findings within the next 5 years could then find applications in the clinic and be fully tested in the next 20 years.

CTS: What are the greatest hurdles (apart from Clinical trials) that these treatments need to pass before they become every day techniques. 


KK: Testing in mammalian model systems will be important. While genes that regulate regeneration and cell proliferation can be activated, it will be critical to establish the safety of activating genetic pathways in models like to mouse, to avoid any unintended consequences.

CTS: Mice tend be to be preferred choice of models when it comes for experimentation and there is evidence for regeneration in them too. Why have you chosen green anole lizards as your model organism?

English: Commons:Category:Anolis carolinensis
Anolis carolinensis
(Photo credit: Wikipedia)
KK: While mammals display limited regenerative capacity, such as the digit tips at neonatal stages (Rinkevich et al., 2011), lizards are the most closely related animals to human that are able to regrow entire body appendages as adults, such as the tail that includes tissues such as skin, skeletal muscle, cartilage, blood vessels, and spinal cord. This capacity for regeneration is also observed in fish (e.g., zebrafish) and amphibians (e.g., axolotl, newt, and frog tadpoles), but not in mammals and birds. The genome sequence of the first lizard, the green anole, was published in 2011 (Alföldi et al., Nature) and molecular analysis of the process in the lizard model became possible. Building on this genome with high coverage annotation (Eckalbar et al., BMC Genomics, 2013), we were able to identify the genes that are differentially expressed along the growing lizard tail.

CTS: Why is it that blastemas do not work in more developed organisms such as mice and humans, when they seem to working well in lesser developed animals such salamanders.
KK: The blastema is not a universal structure formed during regeneration. The original blastema concept arose prior to our understanding of stem cells, and the idea was that there was an undifferentiated mass of multipotent cells localized at the growing tip. The blastema in amphibians was described as avascular. The blastema structure was analogous to embryonic structures such as the elongating presomitic mesoderm or the limb bud.. The regeneration of the amphibian limb involves a region of highly proliferative cells adjacent to the wound epithelium, the blastema, with tissues differentiating as they grow more distant from the blastema. 

Elizabeth Hutchins during a field trip in Panama
Ms. Hutchins enjoying a lighter moment
during her field trip in Panama.
(Photo courtesy: Kenro Kusumi)
One of the key findings of this paper is that regeneration of the lizard tail appears to follow a non-blastema, more distributed model. Evidence for this comes for two major sources: distribution of markers for proliferating cells (PCNA and MCM2O and patterns of gene expression of stem/progenitor cells markers within the lizard tail. In the regeneration of the newt, PNCA and MCM2 immunostaining localizes regions of proliferative growth in the blastema. In contrast, in the lizard tail, PCNA and MCM2 immunostaining is observed is regions of tissue all along the regenerating tail, and skeletal muscle and cartilage differentiation occurs along the length of the regenerating tail during outgrowth. It is not limited to the most proximal regions. Furthermore, the distal tip region of the regenerating lizard tail is highly vascular, unlike a blastema, which is avascular. Genes for stem cell and progenitor cells (hematopoietic, musculoskeletal) are highly expressed in purified lizard satellite cells or embryos, but there is no region of elevated expression within the regenerating tail. Together, these data suggest that the blastema model of anamniote limb regeneration does not accurately reflect the regenerative process in tail regeneration of the lizard, an amniote vertebrate. That is relevant for developing human therapies; if a blastema is not a conserved feature of the regenerative process in amniotes, then we would be pursuing the wrong direction in trying to recreate one in mammals.


References:

Eckalbar WL, Hutchins ED, Markov GJ, Allen AN, Corneveaux JJ, Lindblad-Toh K, Di Palma F, Alföldi J, Huentelman MJ, & Kusumi K (2013). Genome reannotation of the lizard Anolis carolinensis based on 14 adult and embryonic deep transcriptomes. BMC genomics, 14 PMID: 23343042

Rinkevich Y, Lindau P, Ueno H, Longaker MT, & Weissman IL (2011). Germ-layer and lineage-restricted stem/progenitors regenerate the mouse digit tip. Nature, 476 (7361), 409-13 PMID: 21866153

Hutchins, E., Markov, G., Eckalbar, W., George, R., King, J., Tokuyama, M., Geiger, L., Emmert, N., Ammar, M., Allen, A., Siniard, A., Corneveaux, J., Fisher, R., Wade, J., DeNardo, D., Rawls, J., Huentelman, M., Wilson-Rawls, J., & Kusumi, K. (2014). Transcriptomic Analysis of Tail Regeneration in the Lizard Anolis carolinensis Reveals Activation of Conserved Vertebrate Developmental and Repair Mechanisms PLoS ONE, 9 (8) DOI: 10.1371/journal.pone.0105004

Wednesday, October 8, 2014

Binge on sugars and yet stay fit [Coffee-byte]

Eat chocolates but not put on weight
Image credit: itimes.com
Imagine a life where you could eat all the sweets, chocolates and junk food in the world and not bother about putting on weight. Well, it is not some weight loss diet or a strict exercise regime that we are promoting. This is you leading your normal life, going to work, lazying on weekends, spending time with your family and friends, but with one additional mutation inducted in your Nrf2 gene

While this is far from reality for humans, at least in the near future, roundworms in Dr. Sean Curran's lab at the University of Southern California are enjoying this life style even today right now even as you read this post. This happening because the roundworms (Caenorhabditis elegans) carry a mutated version of the SKN-1 gene, which makes it hyperactive. The excess activity of the gene allows the worms to eat a high sugar diet and still not gain any weight while regular worms that do not carry the mutation became obese on a similar diet. 

Crawling C. elegans hermaphrodite worm
Crawling C. elegans hermaphrodite worm (Photo credit: Wikipedia)
Humans possess the Nrf2 gene which is similar in nature and function to the SKN-1 gene and therefore, Dr. Curran is confident that his findings will eventually be effective in humans as well. Luckily for him, the Nrf2 gene has been well characterized in humans and the Nrf2 protein produced by the gene is involved in the damage repair machinery of the cells. The gene has also been studied excessively, since increased activity of the gene has been linked with cancers. 

Therefore, a genetic treatment for mitigating the effects caused by your sweet tooth might take a little longer to come in. Nevertheless, it is a start. But until the cure comes in, exercising should be a good resort you could take. 

Source: 
Pang, S., Lynn, D., Lo, J., Paek, J., & Curran, S. (2014). SKN-1 and Nrf2 couples proline catabolism with lipid metabolism during nutrient deprivation Nature Communications, 5 DOI: 10.1038/ncomms6048

Monday, October 6, 2014

Why viruses are not in our good books?

For all their amazing abilities of being able to survive outside their host, replicate in large numbers and still not be called 'living', viruses have failed to get some positive reviews for themselves. This is likely to be because the term virus is associated with some of the most scariest diseases in human history. Influenza, AIDS, SARS and the recent spread of Ebola, all have their roots in the term 'virus'. Yet, today, we will not dwell on how bad viruses are or the havoc they can cause. This post is more about how intelligent can viruses be! 

Parasitoid, Microplitis infecting larvae
Microplitis infecting its host worm.
Source: upclosephotography.blogspot.com
Although most viruses are associated with harmful diseases that are caused as a result of infection, there is also a large family of viruses who have a friendly association with their hosts. Called Polydnaviruses, these viruses have long been known to exist, mutually, with their hosts, the parasitoid wasps (which rely on smaller insects such as worms for their reproduction). On gaining maturity, the parasitoid wasps lays its eggs in the body of a living worm, where they incubate and hatch after the gestation period.

When the wasp lays eggs into the the worm, it is quite natural that the worm's immune system will detect a foreign body and act against it. While the wasp has no control over the immune system of the worm, it is the Polydnavirus, that it has injected, along with its eggs, that it depends upon to keep its eggs safe.

Polydnaviruses have just two main missions in their life cycle. 









1. Help its host infect the worm necessary for its survival.   

Polydnaviruses are capable to creating some unique proteins that can bring down the first line of defence in the worm body, the hemocytes. After infecting, the cells of the host worm, the virus quite generously chooses to only weaken the worm's immune system so that the wasp eggs can develop. This is in stark contrast to usual virus behaviour that we are quite used to seeing, where it overtakes the host cell machinery to make millions of its own  kind, ultimately resulting in the death of the host. 

Rather, Polydnaviruses also have some other tricks up their sleeve to help them combat the immune system. Not only can these viruses produce proteins that can inactivate attacks made upon the viral infection, they can also abort apoptosis (programmed cell death), the cell's self-destruct button to keep the infection from spreading further. While the virus seems to be putting in a lot of effort into safeguarding the interest of its friend, the parasitoid wasp, there is some selfishness behind this great act of generosity. The clue to this lies in the second aim of the polydnaviruses 

2. Ensure that it passes itself onto the next generation of its host.

To accomplish their second mission, Polydnaviruses have developed an interesting scheme of their own. Over generations of mutualism with their hosts, the Polydnaviruses have replicated their genome, broken them into smaller pieces (called proviral segments) and distributed them into genome of their respective hosts. During the process of reproduction, the host must first replicate its entire genome, and while doing so, also copies the pro viral segments. For every egg that the wasp makes, it also copies the complete viral genome into it and this is why the Polydnaviruses are so selfless after hijacking the worm immune system. For every egg that matures into an adult wasp, the virus makes it to the next generation, where it can repeat the same process and ensure its own survival. 

A recent publication Gaelen Burke et al at the University of Georgia and published in PLoS Genetics, has shed more light on how the process takes place. Using next generation sequencing technology, the researchers investigated the genome of a host, Microliptis demolitor and found some interesting facts about the pro viral segments of the M. demolitor bracovirus (MdBV) embedded in its genome. The researchers found that the pro viral segments were packed in the form of circular DNA segments and dispersed at at least 8 distinct locations in the host genome. All these segments were accompanied with unique sequences on either sides that would help them be recognized during reassembly. After reassembly, the virus exists as a provirus in each and every cell of its host but chooses to replicate only in the calyx cells in the ovaries of its host, where once again, it makes its way into the eggs and thus, the next generation. 

No wonder viruses have a hard time getting positive reviews!

Reference: 

Burke, G., Walden, K., Whitfield, J., Robertson, H., & Strand, M. (2014). Widespread Genome Reorganization of an Obligate Virus Mutualist PLoS Genetics, 10 (9) DOI: 10.1371/journal.pgen.1004660