Pooping our way to a healthier tomorrow

Back in December we wrote about the human microbiota and how the microbiome contributes more to the human physiology than we think; disregulation of the microbiome has been linked to chronic C. difficile infection, diabetes, obesity, inflammatory bowel disease, Crohn's disease, and perhaps even autism. Altering the microbiome of affected individuals so that they resemble "healthy" individuals through fecal transplant has been shown to reverse the symptoms of many of these diseases showing that disorder is linked to a change of physiology due to changes in the microbiota (in fact, fecal transplant is more effective than antibiotics in treating chronic C. difficile). Before we go putting fecal transplant on a pede-stool, the scientists and the FDA are still debating how to regulate this bowel movement movement (it's a hard job, but somebody's got to poo it!).

Currently fecal microbiota is regulated as a biological, which means it has stricter control than some other substances and really bungs up both research and treatment of patients who could benefit from it (what a crappy situation). Scientists are arguing that fecal microbiota should be treated as a tissue or given it's own category, similar to what is done with blood.This would allow greater flexibility for both clinicians and researchers to poo what they gotta poo.

Microbiome research is one of the fastest emerging areas of research. Next generation sequencing is pushing this area of research to flush out our understanding of how the microbiome contributes to our physiology. NGS allows rapid analysis of mixed sequences to determine not  only the the species of microbes present, but the exact composition of a microbial community.

To support NGS workflows, Aurora offers the VERSA GENE, a complete walk-away solution for genomics workflows including NGS library preparation (grab your newspaper and take some time for yourself). The accurate liquid handling provides consistency between library preps and this open-system platform allows researchers to leverage different library preparation kits and chemistries available to fully realize everything that NGS can poo. At Aurora we believe that supporting science that can truly make a difference is not just a job, it's our doody!

Let's Talk: Using Genomic Techniques to Better Understand Mental Disorders

In the last few years Bell Canada has started "Let's Talk Day", a day dedicated to increasing conversation and awareness of mental health issues to break through the stigmas associated with mental health. Through "Let's Talk" Bell hopes to encourage those who are suffering to seek help and encourage those who are not suffering to learn more about these very serious disorders. In recognition of this great movement today we are choosing to highlight how genomic studies are helping to give scientists an understanding of the underlying conditions for disorders such as extreme anxiety or depression and helping to direct future pharmacogenic efforts in developing new therapies.

Last year, research published in ACS Chemical Neuroscience demonstrated the role of seratonergic neurons of the Raphe nuclei in mental disorders such as extreme anxiety and depression. Building off this knowledge, a recent paper has used genomic techniques to identify single seratonergic neurons and perform single cell sequencing of transcripts to identify active genes within these neurons. Identification of new targets through a single cell transcriptome approach can direct future studies to potential targets for new therapies; many current drugs only have approximately 60% response rate for many patients.

The authors used YFP, a fluorescent protein, to specifically label the neurons they were interested in so that they could isolate single cells. From single cells they were able to isolate the total mRNA from the cell and build libraries for RNA-Seq. This gave unique insights to how these neurons are regulated and provides valuable information on which receptors are actively expressed under excitatory or inhibitory conditions and provides direction for future drug efficacy studies (for more detailed information read the paper).

Engaging in conversations about mental health and breaking through the stigmas associated with it is a very important topic. At Aurora we are extremely proud to be able to support the kind of research that can make real, tangible impacts on people's lives. For more information about how Aurora supports genomic techniques, visit our website here. To learn more about Bell "Let's Talk" and join the conversation, visit the website: http://letstalk.bell.ca/en/.

Elephant DNA Never Forgets

Although the picture is a little clearer, best not call off Scooby and the gang just yet (don't turn around that Mystery Machine Fred!). A recent study at the University of Illinois Urbana-Champaign researchers have looked at the mitochondrial DNA of isolated elephant populations to look at the breeding history of these species. For some people, this story is interesting enough, for others a dramatic backstory not necessarily highly exaggerated for the purpose of entertainment is necessary. To set the story I choose to do both.

Following the tragic death of Alexander the Great his empire lay in ruins; former generals began snatching up the ruins of the empire and wars broke out over the lands in between kingdoms. In particular Ptolemy and Antiochus met at the battle of Raphia and this is where the mystery begins. Historical accounts go that Ptolemy had 73 African war elephants from what is now Eritrea in North-Eastern Africa, while Antiochus had 102 Asian war elephants. As the account goes, when the two armies met in battle the African war elephants turned around and ran away from the larger Asian war elephants. The problem is: African elephants are generally larger than Asian elephants. So what gives, did Ptolemy just get the short end of the stick at the war elephant store (can you get a refund on some lightly used war elephants?), or was he using a different species of elephant than the historically accepted version (were they savanna elephants or perhaps forest elephants)? Hence the mystery (cue dramatic music).

 

Although research is not necessarily funded just to look into irrelevant historical events, sometimes it has the benefit of making two African war elephants run away with just one Asian war elephant. The research group at the University of Illinois was looking at elephant mitochondrial DNA to study population dynamics and population migration. mtDNA is passed only from mother to offspring, as female elephants stay with the same herd from birth while males may disperse throughout different herds, mtDNA provides a tool to study the breeding dynamics and migration of a specific herd with time. Looking at modern day elephants in Eritrea it was found that the elephants are in fact related to the savanna elephants, and not forest elephants, debunking the explanation that Ptolemy was using a different species of elephants than is historically defined.

Mitochondria have separate DNA from that which is normally contained in the nucleus of our cells. There are several different techniques for specifically separating mtDNA from nuclear DNA during nucleic acid purifications. In order to screen many, many members of a candidate herd to generate concrete evidence of evolutionary relationships, high throughput techniques are necessary to solve the bottlenecks associated with manual sample preparations. At Aurora Biomed we are pleased to work with researchers to develop liquid handling automation tailored to specific applications, and development of high throughput protocols to support research workflows. To find out more about Aurora's liquid handling workstations, visit the website at www.aurorabiomed.com.

Happy New Year From Aurora Biomed!

It's January 2nd. Fresh off the jubilations of New Years Eve we realize that another year is behind us and a new one in front. In keeping with the timeless New Year's tradition of making resolutions, here are some resolutions from Aurora Biomed:

1. Continue optimizing high throughput solutions for our applications including NGLP, SPE, NAP-PCR etc.

We strive to offer customers comprehensive solutions for a variety of applications, to achieve this we want to continue testing our instruments with new applications and work with clients to ensure the best possible fit. Also, we want to develop new exciting features to make our instruments even more versatile

2. Travel

We like to attend conferences every year that represent various different focuses within science. Coming up in January we are exhibiting at the Plant and Animal Genomes Conference in San Diego. Other travel plans include Analytica in Germany, Pittcon in Chicago, and AMP in Washington DC!

3. Meet New People

One of the best parts of being in sales and getting to travel is meeting new people. We want to make an impression on all prospective customers and work with them to ensure that the best solution is found for whatever needs they may have! In 2014 I hope to meet lots of new people.

What are your resolutions? Want to streamline your research to publish more papers? (We can help!) Finally get rid of that pesky tendonitis from too much manual pipetting? (We can help with that too!) Finally lose that last 10 pounds? (Sorry you're on your own!)

Whatever your resolutions are, we hope that 2014 may bring you new opportunities, new friends, and new adventures. And hey, if you do need some lab automation, give us a call!

More about Aurora Biomed: www.aurorabiomed.com

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