Santa's Reindeer Suspected of Performance Enhancing Drug Use

A recent photo of Comet

              It's the time of year that all attention is on Santa and his reindeer; cookies are baking, trees are decorated, the eggnog is appropriately  spiked with rum, and preparation for Christmas night is under full swing at the North Pole. However, this year the attention is on Santa and his reindeer for an entirely different reason. All nine reindeer are currently serving indefinite suspensions from Reindeer Games DLXXIII under suspicion of using performance enhancing drugs. "It's ridiculous!" says Arrow, another reindeer residing at the North Pole, "How can nine reindeer fly around the world in one night? It's obvious that they have an unfair advantage from PED use! How can any of the other reindeer even compete?". This is not the first time that the Reindeer Games have handed out suspensions, most famous is the suspension of Rudolph from the reindeer games in 1939 due to his glowing red nose, an obvious side effect from PED abuse (see Rudolph v. All of the other reindeer, 1939). "It's scary," claims Jingle, one of Santa's elves, "I accidentally kicked snow at Comet and he hauled off and kicked me in the teeth, I had to get dental surgery from Hermey!" Issues with controlling anger is a common reported side effect of anabolic steroid abuse.

"How can nine reindeer fly around the world in one night?

It's obvious that they have an unfair advantage from PED use!"

 -Arrow, an "other" reindeer

Yukon Cornelius addressing the media Monday afternoon

            The Reindeer Games Athletic Committee is currently reviewing the case and will make recommendations for disciplinary actions based on their findings. "All reindeer participating in this year's Reindeer Games have submitted samples for testing. These will be extracted appropriately through solid phase extraction and reviewed by the committee." Yukon Cornelius, chair of the Reindeer Games Athletic Committee, told the media on Monday afternoon. "Until such time as conclusive results have been provided to the committee all nine of Santa's reindeer have been placed under indefinite suspension."
             Aurora Biomed, located in Vancouver, BC, have graciously reached out to the Reindeer Games Athletic Committee offering to lend an automated solid phase extraction workstations for the investigation. "We reach out to everyone at the North Pole in this time of turmoil," said a spokesperson for Aurora, "automation of sample extraction will ensure a speedy resolution to this issue by enabling faster turn around time for sample preparations. Additionally, automation will help ensure all samples are handled with uniformity to make sure that the entire screening process is fair. We want to see a fair and speedy resolution to this issue so the Reindeer Games can continue as planned." Results of the testing are expected later this week. At the time of publication Santa could not be reached for comment.

www.aurorabiomed.com

Its the barcode, the barcode of life.

              A few weeks ago we wrote about a study which used DNA barcoding to analyze the contents of natural supplements. Today let's talk about the Barcode of Life project. The goal of this project is to have DNA barcoding information for every species on earth (yeah, that's a lot!). You might be asking "What's the point of this? I can clearly look at a giraffe and see that it's a giraffe." Well you are right in that respect, but the applications of having a genetic barcode for every species are very wide: information could be used to identify species in poaching cases (Is it endangered? What sub-species is it? What sub-population?), identify pathogens, plant species, the possibilities are very wide. Having information like this could allow researchers, conservationists, etc. to have rapid, specific, accurate identification of species within a few hours.

Nants ingonyama bagithi baba, sithi uhhmm - The barcode, the barcode of life

          DNA barcoding is still in its youth, however, the principle of the technique is sound. In essence, a DNA sequence which is common, but slightly different in every species is sequenced. The slight differences combine to give unique identification of a species, kinda like how all barcodes are made up of many black bars, but the thickness and spacing gives unique identifications. For some genes, the only difference between you and a giraffe is a few nucleotides.
              The scope of DNA sequencing projects is continuing to increase more and more. Another blogger, Nick Loman, has compiled a list of the biggest sequencing projects completed to date, as well as even bigger ones which are yet to be completed (see the list here). Lab automation is necessary for these large projects to expedite manual processes and ensure that the projects are completed on a reasonable timeline. At Aurora we are extremely excited to be a part of this continuously growing movement and can't wait to see where it goes next!

More information about Aurora: www.aurorabiomed.com

Forensic Dismantling Begins at Scene of Hobbit Murder

Gruesome scene uncovered at home of "Lord of the Rings" director Peter Jackson

           Yesterday, The Onion reported the arrest of film maker Peter Jackson following the discovery of a gruesome scene where 15 hobbits were found murdered and dismembered. The discovery sent shockwaves through the Shire, early reports suggest that the captive hobbits were held for lengthy periods of time, beaten and tortured often only being allowed one breakfast per day and completely deprived of elevensies. Authorities have begun thorough dismantling of the scene and are preparing forensic evidence for analysis.
          "I've never seen anything like this," forensic investigator William Bradley told reporters on Thursday, "the amount of work needed to completely process this scene could take months, even years. It will be a long time before we have a good idea of exactly what happened here."
           Jackson was found delusional at the scene claiming that he was hosting friends from the Shire and was preparing a feast for his guests. However, several times during questioning Jackson referred to his victims as "filthy hobbitses" insisting that one of [them] had stolen his "precious". As several of the hobbits appear to have been sexually assaulted, authorities are working to recover DNA evidence, authorities are not clear if Jackson acted alone or if there may be additional suspects in this case. Criminal profiling experts believe that Jackson may have been too delusional to have acted alone. Local authorities are also calling in forensic experts from Middle-Earth who have a better idea of the extreme tortures the victims endured. "The careful collection and cataloging of foot-hair trophies suggests more a more organized and methodical psychosis than Mr. Jackson is currently displaying, we suspect that he may not have acted alone in this case" says Sancho Bulge of the Middle-Earth Behavioral Analysis Unit. Authorities are currently looking into the possibility that Jackson may not have acted alone.

"The careful collection and cataloging of foot-hair

 trophies suggests more a more organized and methodical 

psychosis than Mr. Jackson is currently displaying, we suspect

 that he may not have acted alone in this case"

- Sancho Bulge, Council of Elrond, Middle-Earth Behavioral Analysis Unit

          Collection and processing of DNA evidence will help authorities shed light on this subject. "This kind of sample processing takes time, the number of samples we have to process is large and we need to ensure high quality DNA is recovered for forensic applications. Typically this process is automated to avoid human error and expedite the sample processing, we don't want any mistakes to be made in our analysis of the scene."
              Representatives for Jackson have not made a comment to media at this time. A latern release ceremony has been arranged over the Brandywine river in memorium of the victims.

Note: The Onion is a fictitious news source, Peter Jackson did not murder 15 hobbits and is not in police custody. Hobbits are a fictitious character from the fantasy series "Lord of the Rings" they do not exist. However, if they did exist, the VERSA NAP workstations would be able to extract their DNA for forensic applications described above. Pretty cool huh? We can purify hobbit DNA.

Read the original post on The Onion: http://www.theonion.com/articles/grisly-remains-of-15-hobbits-discovered-in-peter-j,34754/
Find out more about Aurora Biomed: www.aurorabiomed.com

Snakes are cool!

         Ask any ten year old boy and he'll tell you straight: snakes are cool. Little does that ten year old know that that statement is actually very profound from a scientific point of view. Recently, the assembled genome of the Burmese python was published in PNAS. The reason this is so profound is examining the genes of the python may lend clues to our own evolution. As crazy as this sounds, its true. For the most part we have the same genes as a python, differences in gene copy number and expression level/differential expression in different tissues is the reason that we are human and a snake is a snake.
           One of the things that the Burmese python is known for is its ability to consume prey larger than it is. We have all heard of its ability to unhinge its jaw and slowly consume very large prey, however, the physiological processes that accompany this ability are "cool" to say the least. The python is able to greatly increase metabolic gene expression following a meal to ensure that the prey is properly digested. Not only that, but several organs actually increase in size during digestion returning to their normal size approximately 1 to 2 weeks later. Understanding the genetic processes that allow these changes to take place may help us to come up with new treatments for human diseases.

          As the power of next generation sequencing continues to increase new genomes are being published at an unprecedented rate, uncovering clues not only about evolution but also related to human issues. Recently the genome of the king cobra was published in order to examine genes involved with venom production in the snake. This is the second venomous vertebrate genome published to date; the first was the platypus, yes that's right, even the platypus has its genome published.
          The next step in acquiring knowledge about the secrets of life is to continue to sequence genomes. Large consortium projects such as the 1,000 genomes project will allow more comparative genomics to tease out the subtle differences that make us who we are. As the scope of these projects continues to increase the needs of sequencing providers to process sample libraries is also increasing. To meet this demand Aurora offers the VERSA NGLP liquid handling workstation. Find out more here.

More about Aurora Biomed: www.aurorabiomed.com

It's a community thing

        What if I told you that 90% of your genome isn't human. What if I told you that for every human cell, your body hosts 10 bacterial cells. What if I told you that bacteria don't just live in us, they are a part of us. It's true, bacteria outnumber us 10 to 1 in our own bodies, their DNA and biochemistry contributes to our own biochemistry as a greater "super-being". That's right, we are all super-beings made up of part human, part bacteria. It doesn't seem so bad when someone calls you a super-being does it? The truth is bacteria are as much a part of us as they are just "on us". Studies have linked our bacterial populations to many diseases such as inflammatory bowel disease, diabetes, obesity, chronic C. difficile infection, and even tumorigenesis in cancer. The genes and biochemistry of bacteria contribute to all these things.
          How you ask? Different sub-populations of bacteria contribute different aspects to your microbial community. Just like the TV show "Community" different sub-populations play different roles in the group; depending on who is or isn't present, the whole group can work well together, or fall apart in a hilarious episode of mayhem (it isn't as funny when it happens in real life...). If one role is over or under represented the entire system can be thrown off leading to a disease state.
           Recently these conditions have had good success being treated by restoring the microbial balance to that of a "healthy" situation. Obesity has been reversed, insulin sensitivity increased, and bowel diseases such as IBS and Crohn's have been treated through fecal transplant therapy. Yup, it is disgusting as it sounds but it goes to illustrate how important a healthy microbial community is to our overall health. Transplant not only temporarily helps to change the recipients microbial population but these changes are retained over time essentially transplanting a healthy microbial community and resulting in real biochemical changes in the host due to different interactions with microbes.
           It is being increasingly revealed that our microbiome plays a huge role in our body's physiology. Microbiome studies have greatly increased in number in recent years and it seems as though we are just beginning to uncover the extensive interplay between our body and our microbes. As the analytical powers of Next Generation Sequencing continue to increase we will be able to solve more and more of these mysteries. Prospective samples for NGS studies need to be handled with uniformity to ensure that no one species is over or under represented due to processing error. Automation helps ensure that each sample is handled in exactly the same way and helps remove sources of error associated with manual techniques. To learn more about Aurora's automated NGS library prep workstation, click here.

More info about Aurora Biomed: www.aurorabiomed.com

A Little Golden Nugget

A Little Golden Nugget

Pope Francis blessing a sample of Golden Rice in the Phillipines

          In North America we are lucky. For the most part we don't have to worry about where our next meal will come from, diseases associated with malnutrition are much more rare. This is not the case in the developing world where food security is still an issue of great concern. According to the Declaration of Human Rights put forth in 1948 by the UN "food security exists when all people, at all times, have access to sufficient, safe, and nutritious food to meet their dietary needs and food preferences for an active and healthy life". However, upwards of 250,000 to 500,000 children in the developing world go blind every year due to Vitamin A deficiency and up to half of these die from the condition. Vitamin A is found in many foods: carrots, spinach, mango, papaya, eggs and cheese, all of these foods can act as sources for Vitamin A, but lack of access to nutritious food drives the problem in many parts of the developing world.
 

World distributions of Vitamin A deficiency

            In the early 2000's a potential solution was created: Golden Rice. The rice was genetically modified by a team in Switzerland to include the synthetic pathway of  a Vitamin A precursor. As rice is a staple food in many of the countries where endemic Vitamin A deficiency is a serious issue, this presented a viable solution. However, Golden Rice has faced much opposition throughout its development. Some fear that cultivation of Golden Rice will lead to wider acceptance and adoption of other GMO's, others argue that allowing corporate control of food production in this countries actually undermines food sovereignty and would help perpetuate the cycle of poverty. In either case, all the implications of adopting GMO products must be weighed against the potential benefits to society.

Golden Rice (right) compared to normal rice (left)

          Earlier this year Pope Francis blessed a sample of Golden Rice in the Philippines shortly after protesters destroyed a field of the grain. The benefits to mankind outweigh the negative aspects of this GMO crop which is why Pope Francis chose to bestow his blessing on it. Other GMO's act to add resistance to herbicide or disease, in general acting to benefit the farmer and not the consumer. In this case just the opposite is true, Golden Rice has been supported by a variety of NGO's and is designed to benefit the people and not put profits in the pockets of large corporations. As with adoption of any technology, the benefits must be weighed against the risks.
          Production of GMO's is a complicated and arduous process. Regardless of personal views of the risks and benefits of GMO's, thousands of brilliant scientists continue to work on developing new varieties; some may benefit the producers, some may benefit people, and some may only help to add to the bottom line of large corporations. Aurora's goal is to help the scientist, to expedite sample preparation in basic lab operations such as DNA extraction, PCR setup, and DNA sequencing efforts necessary for development of new crops whether they are created through genetic modification or conventional breeding programs. Automating the techniques associated with the scientific process helps to drive development cycle and bring new, beneficial products to market faster. To find out more about how Aurora helps drive various applications visit our webpage.

Find out more about Aurora: www.aurorabiomed.com

Telling Your Future

Telling Your Future

            A few weeks ago we wrote about the debate surrounding genetic testing in newborns (read "The  Great (DNA) Debate" here). Now we ask, how much of your genetic future would you like to know? Some infantile diseases require immediate action; diseases like phenylketonuria are devastating in newborns, early detection and treatment can stop the progression towards serious disease. But what about a slightly higher risk for cancer? Would you live your life differently knowing what your future may (or may not) have in store for you? Should screening be performed for untreatable diseases knowing that the only information an individual could gain would be the knowledge that they are going to die. Sure, it is the responsibility of the physician to share this information, but would you want that knowledge hanging over your head for your whole life?

           How much information we should have about ourselves (and when to have it) is a debate that is still on-going. The issue is not only personal information relevant to yourself, but who else will have access to it? Where is technology headed? Will we identify genetic markers commonly found in criminals so the CIA could track those people throughout their life? (Throw on your conspiracy shoes people because this just got real!) Could entire career tracks be predicted and "optimized placements" be made based on genetic predispositions?
         The fact remains that newborn screening is an extremely beneficial process and a great benefit to mankind. Where NGS technologies go from here remains to be seen, I for one would embrace more comprehensive testing of newborns to increase the quality of life for my future children and their children but am wary of what could be done with this information. Regardless, labs require the power to process the samples, and Aurora is happy to provide that power. How you ask? Why with the VERSA 1100 NGLP of course!

Aurora Biomed: www.aurorabiomed.com

Don't Judge a Bottle by its Label

Don't Judge A Bottle By Its Label

Ginko - Yeah, I didn't know what it looked like either...

Don't judge a book by its cover, or so the saying goes. This is especially true when the title of the book has nothing to do with the topic, who would guess Moby Dick was about a whale? You might wanna throw a picture of a whale on the cover there Melville, just so people don't get confused! That's why its easy with herbal supplements, the label tells you exactly what's in the bottle, if you buy a bottle a ginko root, boom it says it right on the bottle!

It turns out it might not be that simple. A recent study published in BMC Medicine used DNA barcoding techniques to look at the actual contents of 44 herbal supplements and compared them to their living relatives.To do this, researchers must extract the DNA, amplify a small region of the DNA which contains changes unique to that species (like a barcode on a box of cereal, get it?!), then sequence the DNA to see the specific changes and identify the species. In the case of the ginko root, the researchers found it was contaminated by black walnut, the nerve!

This paper has received a lot of attention, and not necessarily all of it positive. There have been calls to have the paper retracted saying that the use of DNA barcoding is not the appropriate technique for this application and that the researchers made errors while doing so. The critics also call for a more stringent peer review process to ensure that the appropriate changes are made to the paper.

DNA barcoding is a fairly well established technique. It is less onerous and time consuming than RFLP and can be used to deliver high quality reliable results. Not only that but the critics have used DNA barcoding in their own, similar studies. Not to mention that BMC Medicine does require publications to be peer reviewed by two "experts" in the field which is fairly standard for medical journals. Maybe the critics are upset because they can no longer think about their daily ginko hit in the same way...

Studies like this one are becoming more and more common, and the criticisms are just as common. The new generation of genomic techniques has enabled us to look at things at the finest levels. However, the techniques leading up to analysis have not changed, DNA extraction and PCR remain largely the same since the techniques were first described. To push the industry forward, liquid handling robotics enable faster, more precise preparation of samples and help push from raw input to results faster. For more information, take a look here.

Read the original paper in BMC Medicine: http://www.biomedcentral.com/1741-7015/11/222

Find out more about Aurora: www.aurorabiomed.com

Off to Phoenix!

 Off to Phoenix!

           Next week we will be off to beautiful Phoenix, AZ to attend the 2014 Annual Meeting of the Association for Molecular Pathologists. We will be rubbing shoulders and hob-nobbing with some of the brightest pathologists in America. Don't be jealous, it's not forever, the conference only lasts for 3 short days, so we will be out of the heat and back to rainy Vancouver in no time!
            We are very excited to attend this conference. Increasingly, molecular pathology is using genomic techniques to screen for diseases. This includes DNA microarrays, DNA sequencing, and other techniques which allow rapid and highly accurate diagnosis. The field of molecular pathology is on the fore-front of medicine and we are excited to see the growth this rapidly advancing field has undergone.
             At the show we hope to do some showing off of our own. We will be showing our VERSA 10 NAP workstation and the VERSA 1100 NGLP workstation at our booth. These workstations help enable clinicians, researchers, and masters of molecular pathology alike to keep up with demands placed by the rapid growth of this field by increasing walk away time and allowing them to focus on more important things like making sure sick people get healthy! Don't stand there and do it yourself, let VERSA do it!

More information about AMP: http://www.2013amp.org/
Aurora Biomed: www.aurorabiomed.com

What's that smell? (It's you!)

What's that smell? (It's you!)

          When you think of smell you think of lots of different things: dogs,  sharks, Nelson from The Simpsons. One critter you don't think of is the mosquito. Well put that idea aside because as it turns out the mosquito can smell, specifically it can smell YOU! Researchers have found that the Anapheles mosquito, the main vector for malaria, appears to have evolved a specialization for sniffing out humans. Over the years Anapheles gambiae has specialized in finding and feeding on humans; kinda like Jaws but more annoying and itchier.

            The infected female anapheles transmits malaria when feeding on a healthy individual. The parasites enter the bloodstream and quickly infect the host blood cells causing the disease we know as malaria. Malaria is a worldwide problem affecting  219 million people in 2010 as estimated by the World Health Organization. Although the primary region affected by malaria is sub-Saharan Africa, the disease is far reaching to even the United States.

            In the paper (found here) scientists sequenced and analyzed the genome of Anapheles gambiae as well as Anapheles quadriannulatus, a related species which does not appear to preferentially feed on humans. The researchers found that there was a combined effect of mutations in some (what I'm going to call) "smell receptors" in the mosquito's antennae (it smells with its antennae? gross) as well as an abundance of other "smell receptors" that help it specifically smell humans. (This is a huge simplification, for more info read the paper!)

            Studies like this one are rapidly changing our understanding of disease and disease transmission. Driven by the power of next generation sequencing, our ability to undertake these projects is increasing every day; a project like this would have been impossible not so long ago! However, with great sequencing power comes great necessity for sample processing. And we all know what spiders do to flies

Read the original paper:  http://www.biomedcentral.com/1471-2164/14/749/abstract

More about Aurora Biomed: www.aurorabiomed.com

The Great (DNA) Debate

The Great (DNA) Debate

             At the recent ASHG meeting one of the hot-button topics was DNA sequencing in newborns. Currently, the states require the screening of minimum 21 genes in all newborn babies for hereditary disease; having information about the babies A's, T's, C's and G's can immediately improve their treatment to make sure they can learn their ABC's. As DNA sequencing technology continues to improve we may be able to completely sequence the entire genome of a newborn child. This may help answer questions like will the child succumb to the family predisposition to diabetes or heart disease, giving valuable information about potential for diseases and other information that could help discover markers and treatment for diseases (or find a genetic marker for being devilishly handsome).

Terminator, as portrayed in the movie "Terminator"

             

         The idea of complete genome sequencing for newborns is not without arguments against it. Where and how will this information be stored? (Please not on a computer named Skynet!) How long will it be stored for, and who will have access to it? Will the information be strictly for clinicians? Could researchers use it to help drive research? Will insurance companies deem individuals ineligible for insurance, or base insurance premiums off of this information?

               We live in an exciting time where technology is moving at a blistering pace. As much as we need the innovators pushing us forward, we need the critics urging caution (before a cyborg from the future travels to the past to kill our mother before we are born). Where is the line drawn? Will the future consist of a race of genetically engineered superhumans? The debate on how much information should be taken from DNA sequencing projects and what should be done with that information is taking place right now.

              Speaking of DNA sequencing and robots (http://www.aurorabiomed.com/nucleic-acid-isolation.htm) there already exists robots for the automatic extraction of DNA from human tissue. This helps researchers by freeing up time for them to do other tasks while DNA can be extracted from many samples at once, with minimal concern of time travel and minimal danger for prospective mothers.

More information about Aurora Biomed: www.aurorabiomed.com