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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RNA Vaccines: Safer and Better Than Pathogens

  • Polio Virus Accidentally Discharged by GlaxoSmithKline  
  • Anthrax Accidentally Shipped to Numerous Labs
  • New RNA Vaccines are Viewed as Much Safer and Better

Polio Virus Accidental Discharge

Polio virus is pretty but highly pathogenic. Taken from dr.marahimi.com.

Polio virus is pretty but highly pathogenic. Taken from dr.marahimi.com.

The genesis of this blog about safer, better vaccines using RNA instead of pathogenic organisms was an incident that received very little attention in the US but was big news in Europe and—frankly—scared the bejeezus out of me. London-based GlaxoSmithKline (GSK) acknowledged in a report that its vaccine production personnel in Belgium dumped 12 gallons of liquid contaminated with poliovirus into the local sewage treatment plant and subsequently into the Lasne River. Yikes!

A spokesman is quoted as saying that there was “an accidental discharge of cleaning solution that had been used to sanitize equipment used in the manufacture of polio vaccine.” However, chances of anyone developing polio from being exposed to the water were said to be very low, “given the high level of dilution and high level of public vaccination”—vaccination against polio is compulsory in Belgium. That may be true, but the issue is increasing safety, as you’ll see from what follows here.

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Gene-Expression Biomarkers Can Detect Depression

  • First-ever Lab Test for Depression Found Using RT-PCR
  • FDA Approval as Diagnostic Possible by Early 2016
  • Huge Potential Market as 1-in-10 US Adults Suffer from Depression

While it’s normal for everyone to occasionally feel blue or sad, prolonged bouts of depression that interfere with normal life are indicative of a serious mental health issue. While there are numerous forms and differing severity of depressive disorders, as described at a National Institute of Mental Health (NIMH) website, only two factual aspects of this illness really stand out in my opinion:

Redder countries have higher depression rates. Bluer countries have lower depression rates. Taken from The Washington Post.

Redder countries have higher depression rates. Bluer countries have lower depression rates. Taken from The Washington Post.

  • Depression is a very common illness. The Centers for Disease Control and Prevention estimates that 1-in-10 US adults suffer from depression, which reportedly costs close to $50B annual in lost productivity in the work place. Globally, more than 350 million people of all ages are afflicted with depression, according to recent statistics from the World Health Organization (WHO). By the year 2020, WHO estimates that depression will be the second leading cause of “lost years of healthy life”, following heart disease. Incidentally, as seen from the map below, depression rates around the world vary significantly among countries.
  • Depression is diagnosed based on the patients’ self-report of their symptoms and the evaluation of one or more structured psychiatric interviews with the patient by a psychiatrist, psychologist or primary care physician. The absence of direct, non-subjective measures of depression can lead to relatively lengthy time-to-treatment, non-reporting, or—sorry to say—fraudulent claims and/or treatments based solely on what is said as opposed to what is objectively measured.

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Liquid Biopsies Are Viewed as “Liquid Gold” for Diagnostics

  • Invasive Needles and Scalpels Seen as Passé
  • Noninvasive Sampling Advocates Focusing on Circulating Tumor Cells (CTCs) 
  • New Companies are Pursuing the Liquid Biopsy “Gold Rush”

Biopsy Basics

Ultrasound is a real-time procedure that makes it possible to follow the motion of the biopsy needle as it moves through the breast tissue to the region of concern, as discussed elsewhere (taken from oncopathology.info via Bing Images).

Ultrasound is a real-time procedure that makes it possible to follow the motion of the biopsy needle as it moves through the breast tissue to the region of concern, as discussed elsewhere (taken from oncopathology.info via Bing Images).

As defined in Wikipedia, a biopsy is ‘a medical test commonly performed by a surgeon or an interventional radiologist involving sampling of cells or tissues for examination.’ Biopsies can be excisional (removal of a lump or area), incisional (removal of only a sample of tissue), or a needle aspiration (tissue or fluid removal). Despite the value of these traditional types of biopsies, they are more or less invasive, lack applicability in certain instances, and require accurately “going to the source” of concern, as pictured to the right, for ultrasound-guided breast cancer biopsy. Better methodology is highly desirable and is the topic of this post. By the way, if you want to peruse a lengthy list of scary risks associated with various type of common invasive biopsies, click here to see what I found in Google Scholar by searching “incidence of complications from biopsies.”

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Top Picks from Tri-Con 2015

  • “Honey I Shrunk the qPCR Machine” Tops Presentations
  • High School Student Wins Popular Vote for Best Poster
  • BioFire Defense FilmArray is More Interesting Exhibitor
  • Extra Bonus: Swimming with the Sharks

The 22nd International Molecular Medicine Tri-Conference—better known as Tri-Con—took place on Feb 15-20 in San Francisco, where I and 3,000+ other attendees from over 40 countries took part in a jam-packed agenda. In this blog I’ll briefly share my top 3 picks—and an “extra bonus”—but first some insights into the challenges involved in navigating a large conference like this.

The first challenge was scoping out four simultaneously occurring “channels”—diagnostics, clinical, informatics, and cancer—to select as many interesting items as possible from all the presentations (500), panel discussions (30), posters (150), and free “lunch-nars.” The new Tri-Con’15 app with a word and name-searchable agenda (including abstracts) made this easier than previous years. I was even able to put selected items into a calendar/to-do list with 15-min reminder alarms—very slick and convenient. Every big conference should have an app like this!

The second challenge came once I was physically onsite. It took a bit of effort to navigate from one room to another in the huge, multi-room Moscone Center without GPS guidance. I was also struggling to make it to the talks and events on time without getting hijacked by bumping into friends—which happened a lot.

The third and final challenge had to do with posters. Given all of the other exciting options during the conference, I really had to focus to stay on-task and make sure I was present at my poster at the specified times, yet alone try to get around to the other posters of interest. This was definitely not easy, since my poster entitled Pushing the Limits of PCR, qPCR and RT-PCR Using CleanAmp™ Hot Start dNTPs attracted a steady stream of interested visitors. But that’s a great challenge to have, so I can’t complain too much.

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2014 BioGENEius Challenge Top Honor Announced

  • Premier Competition for High School Students Culminates at BIO International Convention
  • Winner, Emily Wang, Developed New Fluorescent Proteins to Improve Biosensing
  • Her Grandmother’s Battle with Cancer Inspired this Award Winning Research

I don’t know about your science achievements while in high school, but mine were limited to getting up early on Saturdays to go to Biology Club to dissect worm, starfish and cat specimens to study anatomy—and trying not to pass out from noxious formaldehyde preservative! Thus, I am constantly amazed by the level of complexity and maturity that I see in young science students today, and I always look forward to seeing who will win the annual BioGENEius Challenge.

The BioGENEius Challenge is the premier competition for high school students that recognizes outstanding research in biotechnology. The Challenge is organized by the Biotechnology Institute, a U.S. based nonprofit organization dedicated to biotechnology education. Its mission is to engage, excite and educate the public, particularly students and teachers, about biotechnology and its immense potential for solving human health, food and environmental problems.

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San Diego Shines Among Top 10 Biotech Product Innovators in 2014

  • Five of the Top 10 Biotech Products Picked by The Scientist were Developed by San Diego Companies
  • Most of the Innovations Involve Genomics
  • List Includes Several Repeat Winners as well as new Leaders in Cutting-Edge Technology

Recently The Scientist published its annual list of top 10 innovations for 2014. There are several repeat winners this year, including Illumina with two new sequencers and Leica Microsystems with a new 3D superresolution microscope. There are also a number of exciting new products associated with cutting edge technology in fields like human organ models and a Twitter-like site to handle the ever-increasing number of scientific publications. One of the most notable attributes of this year’s list, however, is that half of the award winning companies are based right here in San Diego.

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You and Your Microbiome – Part 2

  • Global Obesity Epidemic is Linked to Gut Microbiome
  • DNA Sequence-Based Microbiomes Accurately Associate with Obesity
  • Blue Agave Margaritas Contain Beneficial Gut Microbes
  • Investments in Microbiome-based Therapies on the Rise, but is there Hype?

Last August, my post entitled Meet Your Microbiome: The Other Part of You dealt with growing recognition that trillions of microbes—mostly bacteria but also fungus—reside in and on each of us, and influence our health status. Moreover, the compositions of these microbiomes change with our diet, what we drink or breath, and who we contact—family, pets, and close friends.

Since then, I’ve collected a string of microbiome articles delving into the implications of this dynamic, symbiotic relationship, and selected some topics that I thought were “blogworthy.” This Part 2, as it were, focuses on overweight/obesity, microbiome therapy, and burgeoning business opportunities.

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Children at Risk from Deadly Respiratory Virus EV-D68

  • Frightening Statistics From CDC
  • CDC Updated U.S. Map of Outbreak & Advice of What to be Aware
  • CDC Develops Rapid Real-Time RT-PCR Test for Detection
  • Some Speculate on Linking Outbreak to the “Southern Border Invasion”

Ebola virus is dominating news reports lately, and perhaps rightly so considering the worldwide impact. Turning our attention, however, to actual incidents of infection and death in the U.S., enterovirus (EV) D68 poses a much greater threat and warrants our attention—especially if you or your friends have young children.

On September 24, Eli Waller’s parents were worried that their 4 year-old son had pink eye and kept him home from school so that he wouldn’t infect other children. He seemed otherwise healthy. What happened next was shocking.

Eli Waller (Credit Andy Waller, via Associated Press). Taken from NY Times.

Eli Waller (Credit Andy Waller, via Associated Press). Taken from NY Times.

‘He was asymptomatic and fine, and the next morning he had passed,’ said Jeffrey Plunkett, the township’s health officer. ‘The onset was very rapid and very sudden,’ quoted the NY Times.

A week later the Centers for Disease Control and Prevention (CDC) confirmed that Eli had been infected with EV-D68.

EV-D68 was seen as early as August of this year as hospitals in Missouri and Illinois reported increased visits from children with respiratory illness. Soon, the virus was identified in 43 states and detected in 594 patients, 5 of which died.

After reading this very sad—if not frightening—story, I decided to research EV-D68 for this “hot topic” blog, which I’m dedicating to little Eli Waller.

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October is Down Syndrome Awareness Month

Down syndrome remains the most commonly diagnosed chromosomal condition with approximately 6,000 afflicted babies born in the U.S. each year. This means that Down syndrome occurs in about 1 out of every 700 babies.

In recognition of Down Syndrome Awareness Month, this post provides information about Down syndrome taken from the U.S. Centers for Disease Control (CDC) and Prevention website. It also provides a personal story about John Nguyen, a coworker at TriLink, whose first born son, Jordan, has Down syndrome. I’d like to first introduce the Nguyen’s story and then continue on with an overview of Down syndrome causes, risk factors and diagnosis.

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