Zoning in on Zika

  • Zika Virus Infection is Spreading from Africa and South East Asia to Brazil, UK and USA
  • Early Detection is Enabled by Quantitative RT-PCR
  • Smart Surveillance Systems are Available, But not Likely to be Used

Zika virus (ZIKV) has rapidly become print headline and TV breaking news for several important reasons that make it blogworthy here, in my opinion. First and foremost is that ZIKV, which is transmitted by infected Aedes aegypti mosquitoes, has been linked to 4,000 cases of microcephaly in the past year in Brazil alone. Microcephaly is a serious and often fatal condition in which babies are born with unusually small heads. Guillain-Barré paralyzing syndrome may also be associated with ZIKV.

A researcher in Brazil with Aedes aegypti mosquitoes. Taken from nytimes.com  

A researcher in Brazil with Aedes aegypti mosquitoes. Taken from nytimes.com

Much controversy over Rio 2016. Taken from dailystomer.com

Much controversy over Rio 2016. Taken from dailystomer.com

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Sequencing Trifecta for Top 10 Innovations of 2015

  • Sequencing Sweeps The Scientist’s Top 3
  • Diverse Array of Research and Diagnostic Products Round Out Top 10
  • I Predict 3 Winners for 2016. What Are Yours?
Taken from the-scientist.com.

Taken from the-scientist.com.

Welcome to my first blog of the New Year, 2016! There is a trove of topics in my queue of blogs, and I invite you to check them out every other Tuesday throughout the year. As in the past, this first blog of the year comments on the Top 10 Innovations in 2015 that were picked by a panel of judges and published last month in The Scientist. As a side note, you can also peruse TriLink’s top products of 2015 and predictions for 2016 by clicking here.

When you read about these winners, you’ll find out that 1st, 2nd and 3rd place involve sequencing—a trifecta in parimutuel betting on horse races—that were kind of a sure thing (to continue my analogy to betting) based on sequencing products also being in the top spots in the previous year picks. This preeminence of sequencing will likely continue, as I’ll explain at the end of this blog with my win, show and place bets for next year.

Taken from wikipedia.org.

From wikipedia.org.

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‘Genospirituality’—In the Spirit of the Holidays

This last blog for 2015 comes at a time when many of us are looking forward to the upcoming holiday season to enjoy, in various ways, being or sharing with family and friends, and reflecting thankfully for what we have. We often refer to this as getting into “the spirit” of the holidays, regardless of one’s religious or secular beliefs.

In this context, and with the nucleic acids research-relatedness of my blogs in mind, I thought it would be apropos to tell you a bit about some intriguing research aimed at assessing genes associated with spirituality, by which is meant “an inner search for enlightenment achieved through practices such as prayer [religious] or meditation [secular]”, as elaborated elsewhere.

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Longing for Longevity

  • Craig Venter’s HGI is Slow Moving Compared to Google’s Calico
  • 90 is the New 40: Palo Alto Longevity Prize
  • A 1,000 Year-old Human has Already Been Born, Says Aubrey de Grey
  • Dosing with Modified mRNA for Telomerase Turns Back the Clock—Sort Of

I suspect that thinking about immortality—if not living longer—was something humans mused about ever since they comprehended the notion of death. Why we die and—more importantly—seeking ways to avoid death inevitably followed. Among ancient legends about immortality, I’m fond of alchemists searching for the Philosopher’s Stone (aka elixir of life), although that is predated by several millennia of other mythical attempts by ancient Egyptians, Chinese and Greeks to live forever. Forever is a long time, you may be thinking, and perhaps overreaching even conceptually (although that’s been debated), so how about the likelihood of living a lot longer? If you’re skeptical about living longer and—here’s the catch—enjoying it—here are some scientifically notable folks who think this isn’t too far from reality.

"The Alchymist [sic] in Search of the Philosopher's Stone" painted by Joseph Wright in 1771. Taken from ultraculture.org.

“The Alchymist [sic] in Search of the Philosopher’s Stone” painted by Joseph Wright in 1771. Taken from ultraculture.org.

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Big, Bigger, Biggest—Genomics Projects Go Democratic

  • 1,000 Genomes Project is Big
  • 10,000 Genomes Project is Bigger
  • 100,000 Genomes Project is Biggest—so Far
  • Will 1,000,000 Genomes be Next?

This blog on genomics projects going democratic has—rest assured—nothing to do with US presidential election politics that are already receiving (too much) 24/7 coverage—but rather genomics going from singular to pluralistic. Let me frame this revolutionary change another way to clarify: the much heralded sequencing of “the human genome” (singular) announced in 2001—by competing public and private initiatives—used mixtures of DNA from multiple donors, i.e. “the genome” was actually “the genomes,” all of which are different—in some way. These differences are what make each of us genetically unique. Consequently—and enabled by ever faster and cheaper DNA sequencing—there are increasingly large projects aimed at identifying these genetic variations (aka genotypes or polymorphisms) for association with health or disease status (aka phenotypes). To me, this fundamentally important trending science is definitely blogworthy.

Populations are comprised of genetically unique individuals. Taken from my Wakulla.com.

Populations are comprised of genetically unique individuals. Taken from my Wakulla.com.


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Small RNA is Big Science

  • Most Top-5 Citations in Clinical Chemistry are MicroRNA (miRNA) Biomarkers
  • miRNA Biomarker Bonanza is Predicted by Panel of Experts, Although No miRNA Biomarkers Have Yet Been Approved by FDA
  • Plethora of Potential Short Regulatory RNA Exists Beyond the Typical miRNA Microcosm

I’m always looking for new and hopefully engaging topics to comment on, and a recent “Best of Clinical Chemistry” item featured in a special issue of Clinical Chemistry definitely caught my attention. I wasn’t surprised by MIQE Guidelines being at the top, given that these are the “bible” for doing accurate quantitative PCR (qPCR) that has become a seemingly ubiquitous molecular assay for clinical studies. However, I was totally surprised that the next four “best of” all involved microRNA (miRNA)! Hence today’s blog about these small RNA being big science—play on words intended (although properly speaking I should say short rather than small). Continue reading

DNA Barcodes to Follow Food and Foil Fraud

  • Fork-to-Farm Traceability Proven Practical
  • Uses qPCR Decoding of DNA Barcode “tags”
  • Consumer Concerns May Curb Commercialization

In earlier blogs here I’ve highlighted how sequencing of DNA barcodes has been used to identify fraudulent food sales—such as cheap meat or fish passed off as expensive steak or sashimi—and the same for mislabeled herbal products. Now, I’d like to share with you some nifty work by researchers who have applied qPCR to detect DNA barcode “tags” to follow foodstuff from your fork back to the farm (or farms) from which it originated.

This is not a simple goal to achieve, scientifically, and would certainly have been exceedingly useful, societally, in tracing the origin of food-related incidents such as listeria-contaminated cantaloupes that led to 29 deaths several years ago. In fact, just a few weeks ago there was a deadly outbreak of salmonella linked to cucumbers imported from Mexico wherein 4 people died and 732 were sickened by the bacteria.

They all look the same, but sometimes it’s very importatnt to find out from where they came. Taken from en.wikipedia

They all look the same, but sometimes it’s very important to find out where they came from. Taken from en.wikipedia

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Point-of-Care PCR 2.0

  • Ubiquitome Quickens Pace of POC Apps for Its Freedom4
  • Cepheid Unveils its POC Diagnostics System
  • Hopkins Crew Brews “Coffee Mug-Sized” Gizmo for Fully Automated Chlamydia Testing
Kiwi Dr. Jo-Ann Stanton holding Ubiquitome’s Freedom4 at Tri-Con 2015

Kiwi Dr. Jo-Ann Stanton holding Ubiquitome’s Freedom4 at Tri-Con 2015

Regular readers of this blog will recall a recent byline exclaiming “Honey I Shrunk the qPCR Machine”, which spotlighted the unveiling of startup company Ubiquitome’s first point-of-care (POC) product—Freedom4—developed in New Zealand. Up until then, this far away—for me—exotic island country brought to mind folks fondly nicknamed Kiwi—after the native flightless bird, not Chinese fruit. Mightily impressed by this tiny but powerful qPCR device, I vowed to thereafter keep an eye on these Kiwis’ democratized POC apps enabled by its nifty handheld 4-sample high-performance qPCR device.

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Pseudouridine Biomarker for Breast Cancer

As you are probably aware, October is National Breast Cancer Awareness month. Everyone from the NFL to Yoplait yogurt seems to be engaged in campaigns for fundraising and awareness. I think it’s great to see the extensive community support for this worthy cause. Since breast cancer awareness is top of mind this month, I thought I’d follow up my latest blog about pseurdouridine with a ‘mini blog’ highlighting some interesting research involving a pseudouridine biomarker for breast cancer.

I’d also like to mention that TriLink is participating in Breast Cancer Awareness month. For every order placed in October, TriLink will dontate $5 to Susan G Komen to support the upcoming 3-Day Walk being held November 20-22 in San Diego.

3day

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Profiling Pseudouridine

  • Two New Methods for Sequencing Pseudouridine Leverage Old Chemistry
  • New Methods Reveal ‘Rewiring’ of Genetic Code by Post-Transcriptional Pseudouridination
  • Exciting Future for New Analytical Methods for Modified mRNA
  • Be Sure to Read the Very End of the Blog for a Special Offer!

At the risk of seeming enamored with pseudouridine, which I previously proclaimed—with justifications—to be The 2014 Modified Nucleobase of the Year, recent reports about this fascinating base lead me now to feature it here once again. In that past post, it was pointed out that uridine, which is incorporated into all RNA during transcription of genomic DNA, differs from pseudouridine—historically abbreviated by the Greek symbol Ψ –by how one nitrogen (shown in red below) switches place with a carbon for bonding to the ribose ring. It was also noted that this switch has been long known to be carried out after transcription (aka post-transcriptionally) by an enzyme called—appropriately—pseudouridine synthase, the exact mechanistic details for which remain controversial. This post-transcriptional process that converts U to Ψ at specific positions in RNA is called pseudouridination.
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