Curiously Circular RNA

  • Circular RNA (circRNA) Formation Serendipitously Discovered in 1991  
  • Next-Generation Sequencing Reveals circRNA to be Ubiquitous
  • circRNA can Function as MicroRNA ‘Sponges’ to Regulate Gene Expression

There’s something seductively simple—and curious—about circles, which are unique in having no beginning or end, unlike most other things. On a less philosophical plane, thinking about circles conjures up incongruent memories of delicious doughnuts and geometric definitions from my youthful days going to the neighborhood bakery and diligently taking notes in my high school geometry class, respectively.

donuts

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Genes in Space

  • High School Student’s PCR Experiments Launched to Space Station
  • Program Evaluates Epigenetics Linked to Astronaut’s Altered Immunity
  • Amplyus Has Big Plans for Its Tiny, Low-Cost PCR Device

In my 2013 blog post on the 30th anniversary of the invention of Nobel Prize-winning PCR by Kary Mullis, I ventured to say that PCR of DNA or RNA was the most widely used—and enabling—method for all life sciences on planet Earth. This accolade can now be expanded to extraterrestrial space in view of PCR experiments to be carried out in the International Space Station (ISS) following the April 8th launch from Kennedy Space Center in Florida aboard NASA’s Cargo Resupply Services flight (CRS-8).

Taken from earthkam.org

Taken from earthkam.org

What makes this “out of this world” milestone for PCR even more exciting is that it’s the result of competition among students in high school—yes, high school—to conceive and design PCR-based studies relevant to living in space. Following is a brief synopsis of the program, the winning high school student, and a small startup company with big plans for its low-cost miniPCR™ device.
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National DNA Day 2016 – DNA Dreams Do Come True!

  • Khorana’s Dream of Synthesizing a Gene from Hand-Made Oligos
  • Caruther’s Dream of Automating Oligo Synthesis
  • Venter’s Dream of Fully Automating Gene Synthesis
  • Who’s Dreaming About What’s Next?

DNA Day ImageThis blog acknowledging National DNA Day on April 25th deals with dreams of various sorts, but mainly with gene synthesis, which was only a dream in the 1950s and is now achievable in a way few dreamed possible even a few years ago.

Before I get to DNA gene-dreams that did come true, I want to briefly mention two other dream-like anniversaries. First is the fact that my blog is now beginning its 4th year—yeh!—after its inaugural posting in April 2013 to celebrate 60 years since Watson & Crick’s famous publication of DNA’s helix structure as the fundamental basis for genetic material. Second is this year being TriLink’s 20th anniversary—yeh!—as a leading provider of modified nucleic acids, which co-founders Rick Hogrefe and Terry Beck likely view as their business dream come true. But I digress…

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World’s Smallest Real-Time PCR Device

  • Fits in the Palm of your Hand, and Has Single-Molecule Sensitivity
  • Analyzes 4 Samples, and Can be Modified to do 8 
  • Project Leader Reveals Commercialization Details 

I think we’re all fascinated by catchy headlines touting the world’s biggest, tallest, etc., so a recent publication by Ahrberg et al. in venerable Lab on a Chip claiming the world’s smallest real-time PCR device instantly struck me as blogworthy. It also seemed quite apropos as a follow-up to my previous blogs on the continuing shrinkage, so to speak, of real-time PCR technology for point-of-care qPCR diagnostics or other emerging applications in the field.

This hand-held real-time PCR device, developed by A*STAR Singapore, is amazingly small in comparison to the first real-time PCR system introduced by Applied Biosystems in 1995 that weighed 350 pounds and had a width of 7 feet, thus requiring an entire bench top.

pcr

Left: World’s smallest real-time PCR device. (Taken from Ahrberg et al). Right: Applied Biosystems 7700 real-time PCR system. (Taken from distrobio.com).

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Norovirus: Science Behind the Headline

  • The Virus is Quite Common with 267 Million Cases and 200,000 Deaths Annually
  • RT-PCR is the Detection Method of Choice
  • First Cell-Culture System May Speed Drug and Vaccine Development

We’ve all seen TV news stories about disgruntled passengers disembarking cruise ships returning to port early because of an outbreak of nasty gastroenteritis (i.e. inflammation of the stomach and intestines leading to nausea, vomiting, diarrhea, and stomach cramps). Norovirus (NoV) is the causative agent of these frequently reoccurring “nightmare” cruises, of which 13 have been reported since 2012, sickening some 200-600 passengers. It’s not just limited to cruises, the virus affected 100+ students at a school in Eugene, Oregon last year. And now there’s new evidence for transmission of NoV by eating oysters—which I will therefore not eat in the future.

Taken from counselheal.com.

Taken from counselheal.com.

But perhaps the most NoV-related media attention—and investor ire or litigant action—has been recently focused on gastroenteritis outbreaks at Chipotle—a popular restaurant chain. A criminal investigation is under way at Chipotle, and according to an Associated Press report the company has been served with a federal subpoena.

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Science vs. Semantics—Perspectives Matter When it Comes to Genetically Modified and Genetically Edited Organisms

  • GMO Science and Regulation Have Created Genetic Gordian Knot
  • New Genetic Editing Methods Outpace Rules for Consumer Protection
  • Marker-Based Breeding May Bypass GMOs
  • Soylent Green No Longer A Futuristic Concept
The legendary Gordian knot is a metaphor for an intractable problem. Taken from counter-current.com.

The legendary Gordian knot is a metaphor for an intractable problem. Taken from counter-current.com.

Truth be told, I’ve been vacillating for a long time about writing this blog about genetically modified organisms (GMOs), not for lack of relevance to what’s trending in nucleic acids research, but because it’s an exceedingly complicated subject with no definitive conclusions. There’s a complex mixture of underlying genetic methods, overriding regulatory issues, confused-consumer viewpoints, and balancing global ecosystem vs. humanitarian needs—all interwoven into a modern day version of the Gordian knot.

I’ll now try to unravel some of these tangled perspectives largely to comment on newish nucleic acid-based techniques that are forcing a rethink of regulations in order to better deal with what has become a “regional rat’s nest of regulatory gobbledygook.” Intermixed with the gobbledygook are well-intentioned advocacy groups that nevertheless seem guilty of using irrational—to me—consumer scare tactics.

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Anti-Antisense Makes Sense

  • Antisense Oligos Blocking Antisense RNAs Makes Proteins for Therapeutics
  • New Antisense Approach is Analogous to (-1) x (-1) = 1
  • Drug Company OPKO-CURNA is Taking This Approach to the Clinic

I apologize for the somewhat cryptic headline and mathematical byline for this blog, but they really do encapsulate the following: the underlying molecular biology involves a novel antisense oligo approach to “turn on” a protein, in contrast to all previous use of an antisense oligo to “turn off” a protein. I’ll rationalize the mathematical analogy later.

Taken from nature.com

Taken from nature.com

Recognizing the potential therapeutic value of this “turn-on” mechanism, a startup company with the quirky name cuRNA—a contraction for “cure” and “RNA”—was founded, and was acquired by OPKO—a health care conglomerate—and renamed OPKO-CURNA.

What follows is a condensed version of the full story of yet another example of how basic discoveries in nucleic acid research have “morphed” into new therapeutic strategies, which in turn lead to the genesis of small start-ups that oftentimes get acquired by bigger pharma companies. All of these kinds of stories include variations on a theme that are both informative and interesting—in my opinion.

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Highlights of 2015 Publications Using TriLink BioTechnologies Products

  • Publications Citing TriLink Products Exceed 6,000
  • TriLink Products Showed up at a Rate of One Publication per Work Day
  • Among These Customer Publications, Modified mRNA is Trending
Taken from thetrymovement.com

Taken from thetrymovement.com

From my college classes decades ago, I can still clearly recall—thankfully—many “ah ha” moments. Most importantly is when I crystalized to purity and then confirmed structure by NMR the first compound I synthesized in Organic Chemistry Lab. Another ah ha moment—but on a completely different level—was during a philosophy class when the professor partially paraphrased a quote by Aristotle as “we are what we do.” The full quote given above is even more thought provoking because it ties in the notion of excellence, which I took to heart then, and have attempted to live by ever since.

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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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