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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Could the Current Ebola Outbreak Have Been Prevented?

  • Deadliest Outbreak Yet Shows no Sign of Abating
  • Lack of Funds Hampered Clinical Development of Drugs and Vaccines
  • Treatments Exist so Why are Doctors Left with no Cure to Offer the Infected?

You’ve undoubtedly seen or read ongoing—seemingly continuous—news stories about a serious outbreak of Ebola virus disease (EVD) in Africa, and the two infected American health workers who were brought back to the US for treatment. The title of this blog post is adapted from Sara Reardon’s article in venerable Nature magazine, which I draw from following a brief overview of EVD.

The current Ebola outbreak involving the most dangerous Zaire species has killed more than 1,000 and infected an estimated 1,975 people in West Africa. Sierra Leone, Guinea and Liberia have been hit the hardest, with Nigeria experiencing a handful of confirmed cases and 3 deaths. Tom Frieden, director of the U.S. Centers for Disease Control and Prevention, estimated the outbreak will take three to six months to contain under the best of circumstances. Although the outbreak is the deadliest to date, the chances of infection in the US is remote, albeit theoretically possible that one of the 10,000+ travelers to and from the region over the next three-months could carry the virus back to the US. “Ebola poses little risk to the U.S. general population,” Frieden is quoted as saying. Let’s all hope he’s right.

The current outbreak of the Ebola virus in West Africa has killed more people than any previous outbreak. According to a spokesman from the organization “Doctors Without Borders,” the disease is now “out of control” (taken from via Bing Images).

The current outbreak of the Ebola virus in West Africa has killed more people than any previous outbreak. According to a spokesman from the organization “Doctors Without Borders,” the disease is now “out of control” (taken from via Bing Images).

EVD – Key Facts

Electron micrograph of an Ebola virus virion (taken from via Bing Images).

Electron micrograph of an Ebola virus virion (taken from via Bing Images).

The following selected statements about EVD were taken from a World Health Organization (WHO) website that was updated on April 2014, and should be consulted for further details.

    • EVD, formerly known as Ebola hemorrhagic fever, is a severe, often fatal illness in humans.
    • EVD outbreaks have a case fatality rate of up to 90%.
    • EVD outbreaks occur primarily in remote villages in Central and West Africa, near tropical rainforests.
    • The virus is transmitted to people from wild animals and spreads in the human population through human-to-human transmission, with infection resulting from direct contact (through broken skin or mucous membranes) with the blood, secretions, organs or other bodily fluids of infected people, and indirect contact with environments contaminated with such fluids.
    • EVD is a severe acute viral illness often characterized by the sudden onset of fever, intense weakness, muscle pain, headache and sore throat. This is followed by vomiting, diarrhea, rash, impaired kidney and liver function, and in some cases, both internal and external bleeding. Laboratory findings include low white blood cell and platelet counts and elevated liver enzymes.
    • Severely ill patients require intensive supportive care. No licensed specific treatment or vaccine is available for use in people or animals.

Only 18,959 Nucleotides Encode Much Human Suffering

Simplified schematic drawing of key molecular components of Ebola virus (taken from via Bing Images).

Simplified schematic drawing of key molecular components of Ebola virus (taken from via Bing Images).

Like HIV and other RNA viruses, Ebola is encoded in a relatively tiny genome that nevertheless leads to huge problems for society through complex life cycle/human host molecular biology. As detailed elsewhere, the genome of the Zaire Africa Ebola virus—the most deadly species and the one involved in the current outbreak—is only 18,959 nucleotides in length and contains seven transcriptional units that direct synthesis of at least nine distinct primary translation products: the nucleoprotein (NP), virion protein (VP) 35, VP40, glycoprotein (GP), soluble glycoprotein (sGP), small soluble glycoprotein (ssGP), VP30, VP24 and the large (L) protein. L is the catalytic subunit of the polymerase complex. Ebola virus encodes a multi-protein complex to carry out replication and transcription. Ebola viral RNA synthesis requires the viral NP, VP35, VP30 and L proteins. Each Ebola virus mRNA is presumed to be efficiently modified with a 5′-7-methylguanosine (m7G) cap and a 3′ p(A) tail.

RT-PCR Enables Effective Diagnostics for Ebola Viral RNA

Ebola virus infections can be diagnosed definitively in a laboratory through several types of tests, such as antibody-capture enzyme-linked immunosorbent assay (ELISA), serum neutralization test, and virus isolation by cell culture. Not surprisingly, however, RT-PCR has been demonstrated to be highly specific and sensitive, as outlined in this abstract published by a collaborative team lead by the Diagnostic Systems and Virology Divisions at the United States Army Medical Research Institute of Infectious Diseases:

Viral hemorrhagic fever is caused by a diverse group of single-stranded, negative-sense or positive-sense RNA viruses belonging to the families Filoviridae (Ebola and Marburg), Arenaviridae (Lassa, Junin, Machupo, Sabia, and Guanarito), and Bunyaviridae (hantavirus). Disease characteristics in these families mark each with the potential to be used as a biological threat agent. Because other diseases have similar clinical symptoms, specific laboratory diagnostic tests are necessary to provide the differential diagnosis during outbreaks and for instituting acceptable quarantine procedures. We designed 48 TaqMan™-based polymerase chain reaction (PCR) assays for specific and absolute quantitative detection of multiple hemorrhagic fever viruses. Forty-six assays were determined to be virus-specific, and two were designated as pan assays for Marburg virus. The limit of detection for the assays ranged from 10 to 0.001 plaque-forming units (PFU)/PCR. Although these real-time hemorrhagic fever virus assays are qualitative (presence of target), they are also quantitative (measure a single DNA/RNA target sequence in an unknown sample and express the final results as an absolute value (e.g., viral load, PFUs, or copies/mL) on the basis of concentration of standard samples and can be used in viral load, vaccine, and antiviral drug studies.

According to WHO, Ebola was first detected in 1976 and strides have been made in developing sophisticated tests that can accurately diagnosis the virus, as demonstrated above. There is currently no FDA approved vaccine or treatment for Ebola, but that doesn’t mean one doesn’t exist.

Could Outbreak Have Been Avoided?

Although several vaccines and treatments for Ebola do exist, they are stalled in various stages of testing owing to a lack of funding and of international demand. So, for now, doctors have no cure to offer those with EVD and understaffed clinics must make do with isolating infected people, finding and quarantining their families, and educating the public on how to avoid spreading the disease.

A doctor in Sierra Leone enters the high-risk area of the Ebola treatment center. Credit: Sylvain Cherkaoui/Cosmos/eyevine (taken from Nature).

A doctor in Sierra Leone enters the high-risk area of the Ebola treatment center. Credit: Sylvain Cherkaoui/Cosmos/eyevine (taken from Nature).

The fact that the Ebola virus was identified almost 40 years ago and there’s been ongoing research ever since begs the question, “Was the current Ebola outbreak preventable?” According to Reardon, researchers such as Heinz Feldmann, a virologist at the US National Institute of Allergy and Infectious Disease (NIAID) in Hamilton, Montana, think that the situation could have been avoided. In 2005, Feldmann published a vaccine approach based on vesicular stomatitis virus (VSV) that has since yielded an Ebola vaccine that is effective in macaques. But money is not available to take the next step—testing the vaccine’s safety in healthy humans. Compared with malaria or HIV, “Ebola is just not that much of a public-health problem worldwide”, he told Reardon, and consequently draws little interest from public or private funders.

“What works for Ebola is good old-fashioned public health,” says Thomas Frieden, director of the US Centers for Disease Control and Prevention in Atlanta, Georgia, according to Reardon. “It would be great to have a vaccine, but it’s not easy to do and not clear who you’d test it on.”

There are other possible vaccines as well. The NIAID Vaccine Research Center in Bethesda, Maryland, has developed a vaccine that is carried by a chimpanzee adenovirus, similar to the virus that causes the common cold. The institute hopes to begin testing in healthy people as early as September. Barney Graham, deputy director of the research center, told Reardon that the institute is talking with the Food and Drug Administration (FDA) to speed up the approval process, a position that is strengthened by the outbreak in West Africa.

Biotechnology companies are also developing treatments at a pace that could now be accelerated, as we’ve seen with the ZMapp™ vaccine (discussed in detail below) that arrived in Liberia a few days ago. ZMapp™ was developed by Mapp Biopharmaceutical in San Diego, California. The potenital treament uses monoclonal antibodies (mAbs) that target the virus.

Another potential therapeutic backed by US$140 million from the US Department of Defense, is being tested by Tekmira in Burnaby, Canada. The treatment, called TKM-Ebola, uses chemically synthesized small RNA (siRNA) molecules to bind the virus and target it for destruction. The company began testing TKM-Ebola in humans in January, but in July of this year, the FDA put the study on hold until the company could provide more data on how the treatment works. According to an article in, here’s what the CEO said in response to the FDA news:

“We have completed the single ascending dose portion of this study in healthy volunteers without the use of steroid pre-medication. The FDA has requested additional data related to the mechanism of cytokine release, observed at higher doses, which we believe is well understood, and a protocol modification designed to ensure the safety of healthy volunteer subjects, before we proceed with the multiple ascending dose portion of our TKM-Ebola Phase I trial,” said Dr. Mark Murray, President and CEO of Tekmira Pharmaceuticals. “We will continue our dialogue with the FDA, provided for under our Fast Track status, in order to advance the development of this important therapeutic agent.”

A treatment could be approved by the FDA on a ‘compassionate use’ basis, but that process would have to mesh with a host country’s rules. “A country has to request these things; it’s not something we can force on them,” says Gene Olinger, a virologist at the contract research organization MRIGlobal in Frederick, Maryland. “We have to follow their internal policies for drug development and for testing.” It appears that Liberia, at least, has made such a request and it has been honored.

Coincidentally (or maybe not so much), on August 7, the FDA reduced the full clinical hold on Tekmira’s TKM-Ebola drug to a partial hold, potentially enabling use of the compound in patients. It remains to be seen if the drug will be sent to West Africa to be administered, but such a move leaves some to wonder why the FDA can act so swiftly now but refused to do so back in July, prior to the outbreak.

Mapp’s ‘Mystery’ Ebola Virus Drug Said to be ‘Miraculous’

Major media outlets frequently employ attention-grabbing words—such as ‘mystery’ and ‘miraculous’—so it’s not surprising that these descriptors have been used in recent news reports about two American health workers in Liberia infected with Ebola virus. The Los Angeles Times reported that Mapp Biopharmaceutical’s experimental drug, ZMapp™, was given to Dr. Kent Brantly and Nancy Writebol under circumstances described by the LA Times as “a mysterious treatment.”

With all involved wearing full protective gear, a man believed to be Ebola patient Dr. Kent Brantly is helped from an ambulance at Emory University Hospital in Atlanta on Saturday.

With all involved wearing full protective gear, a man believed to be an Ebola patient, Dr. Kent Brantly is helped from an ambulance at Emory University Hospital in Atlanta. Credit Associated press/WSB-TV Atlanta (taken from LA Times).

Intrigued by the ‘mystery,’ I did some quick research and found ZMapp™ had not been previously evaluated for safety in humans, and “very little of the drug is currently available,” according to LeafBio (San Diego, California), which is Mapp’s commercialization partner.  In fact, the available supply of ZMapp™ is said to have been exhausted, according to a statement posted August 12, 2014 on Mapp’s website. The statement also notes that ZMapp™ is the result of a collaboration by Mapp, LeafBio, Defyrus Inc. (Toronto, Canada)—a biodefense company—and both the U.S. government and the Public Health Agency of Canada.

I went on to read that “ZMapp™ is composed of three ‘humanized’ mAbs manufactured in plants, specifically Nicotiana” (aka tobacco plant—and origin of the word nicotine). In other words, tobacco plants are cleverly repurposed by genetic engineering to produce mAbs suitable for use in humans, as detailed here in a review by Mapp that describes this approach as a “revolutionary advance” in antibody manufacturing.

The tobacco plant: Nicotiana tabacum. Credit Joachim Mullerchem (taken from Science via Bing Images).

The tobacco plant: Nicotiana tabacum. Credit Joachim Mullerchem (taken from Science via Bing Images).

The LA Times also said that CNN reported that the drug had prompted a ‘miraculous’ recovery and that Brantly’s condition improved within an hour after treatment, but that this was greeted with skepticism by longtime Ebola virus researchers.

This skepticism is based on the following series of quotes in the LA Times story:

‘I would be ecstatic if Larry’s product helped save these people, but I also need to be extremely cautious,’ said Thomas Geisbert, a professor of microbiology and immunology at the University of Texas Medical Branch at Galveston.

‘To say the whole thing cleared up in an hour, that doesn’t happen in reality,’ Geisbert said. ‘That’s like something that happens in a movie.’

Dr. Anthony Fauci, head of the National Institute of Allergy and Infectious Disease, said the company had manufactured only three ‘courses’ of the drug, and that two of them were provided to the American patients.

‘This was the first time it was put into humans, because all the previous work was done on animals and the results had been encouraging,’ Fauci said.

In closing, I’ll sadly add that it’s unfortunate—to say the least—that funding for timely development of an Ebola vaccine had not been forthcoming from some agencies that knew full well that it was only a matter of time for the next outbreak to occur in Africa. Corporations, however, seem to be stepping in where these agencies may have failed. On Monday, August 11, World Bank announced it will give $200M to help fund the fight against Ebola. Let’s all hope that the current crisis provides the necessary catalyst for that development so as to preclude yet another outbreak and more unnecessary deaths.

As always, your comments are welcomed.

PCR Better than Pap Test for Preventing Cervical Cancer

“Power of PCR” as a Transformative Diagnostic Method

  • FDA Approves Roche PCR Test for Cervical Cancer Screening
  • Automated Test Replaces Pap Test as First-line Cervical Cancer Screening
  • Demonstrates the “Power of PCR” as a Transformative Diagnostic Method

Pap Test

The Papanicolaou test—aka Pap test, Pap smear, cervical smear, or smear test—is a method of cervical screening used to detect potentially pre-cancerous and cancerous processes in the endocervical canal of the female reproductive system. Unusual findings are often followed up by more sensitive diagnostic procedures, and, if warranted, interventions that aim to prevent progression to cervical cancer.

Proper interpretation of microscopic results requires a “trained eye.” This is evident from the representative example shown below, which I found in an online educational textbook and, quite frankly, had trouble discerning the visual keys described in the verbatim caption. Notwithstanding this issue, Pap tests were—until now—the accepted “gold standard.”


Taken from via Bing Images.

The source document for this Pap smear reads as follows. “The cytologic features of normal squamous epithelial cells can be seen at the center top and bottom, with orange to pale blue plate-like squamous cells that have small pyknotic nuclei. The dysplastic cells in the center extending to upper right are smaller overall with darker, more irregular nuclei.”

The eponymous test was pioneered by Georgios Papanikolao, a prominent Greek doctor, who in 1928 was the first to report that uterine cancer could be diagnosed by means of a vaginal smear. However, the importance of this work was not widely recognized until his 1943 publication of Diagnosis of Uterine Cancer by the Vaginal Smear, coauthored by Herbert F. Traut, both at Cornell University Medical College.

ResearchGeorgios Papanicolaou moved to Miami, Florida in 1961 to establish the Papanicolaou Cancer Research Institute at the University of Miami, but died in 1962 prior to its opening. Papanicolaou was the recipient of the Albert Lasker Award for Clinical Medical Research in 1950—this award is sometimes referred to as “America’s Nobels,” as eighty-six Lasker laureates have received the Nobel Prize. Papanikolaou’s portrait appeared on the Greek 10,000-drachma banknote of 1995-2001, prior to its replacement by the Euro.

Cervical Cancer Statistics

Cervical cancer is the second most common cancer in women worldwide, according to an NIH publication in 2007. Country-by-country data for cervical cancer reveal a striking geographical distribution. According to currently available U.S. Centers for Disease Control (CDC) FastStats, cervical cancer mortality in the U.S. in 2010 was ~4,000 or ~2.5 deaths per 100,000 females.

The global statistics provided by Cancer Research U.K. are far more saddening. Worldwide there were more than ~275,000 deaths from cervical cancer in 2010 that accounted for ~10% of female cancer deaths.

Remarkably, mortality rates are reported to vary seventeen-fold between the different regions of the world. By estimating the years-of-life-lost (YLL) by young and middle-aged women (25-64 years old) in different regions of the world, YLL attributed to cervical cancer is the most important cause of YLL for all cancers in Latin America, the Caribbean, and populous regions of Sub-Saharan Africa and South-Central Asia. The overall picture is not very sensitive to the age-weighting function used. The report notes that, since this loss of life is preventable using existing technologies, more health-resource allocation in low income settings is needed.

Pap Test Statistics

Currently available CDC FastStats for Pap test use in the U.S. in 2010 (the most recent year available) are as follows:

  • Percent of women 18 years of age and over who had a Pap test within the past 3 years: 73.2%
  • Number of physician office visits during which Pap tests were ordered or provided: 29.4 million
  • Number of hospital outpatient department visits during which Pap tests were ordered or provided: 2.4 million

Pap Test Recommendations as of 2013

To put today’s blog-post headline about switching from Pap to PCR in perspective, here are snippets from the most recent CDC guidelines and comments made available in a January 2013 press release headlined with “more women getting Pap tests as recommended [but] some women get Pap tests without need.”

  • In 2012, the U.S. Preventive Services Task Force, American College of Obstetricians and Gynecologists and American Cancer Society recommended that women, beginning at age 21, should start Pap test screening every three years.
  • The same groups agree that screening is unnecessary for most women who have had a total hysterectomy (removal of the uterus and uterine cervix) for non-cancerous reasons, or for women aged 65 years and older with several years of normal test results.
  • Studies analyzed Pap test survey data from CDC’s Behavior Risk Factor Surveillance System found the following:
    • The percentage of women aged 18-21 years who reported never being screened increased from 23.6% in 2000 to 47.5% in 2010; however, screening is not recommended for women under the age of 21.
    • In 2010, 58.7% of women aged 30 years and older who had a hysterectomy were still given a Pap test.
    • Because of the Affordable Care Act (aka Obamacare), many private health plans and Medicare now cover certain preventive services, including cervical cancer screening, with no copays or other out-of-pocket costs.

HPV: The Cervical Cancer-Causing Agent and Key to Early Detection

In a landmark publication in 1999 entitled Human papillomavirus is a necessary cause of invasive cervical cancer worldwide, Dutch investigators used PCR data to establish that the worldwide HPV prevalence in cervical carcinomas is 99.7 per cent. They noted that “the presence of HPV in virtually all cervical cancers implies the highest worldwide attributable fraction so far reported for a specific cause of any major human cancer.” More importantly, they presciently concluded that “the extreme rarity of HPV-negative cancers reinforces the rationale for HPV testing in addition to, or even instead of, cervical cytology in routine cervical screening.”

Due in part to technical challenges posed by numerous genotypes of HPV with varying cancer causality detailed elsewhere, and unavoidable time-consuming clinical studies required for FDA approval, it has taken ~15 years for a PCR test to now be poised to displace the Pap test as the primary diagnostic approach for early detection of cervical cancer.

Those of you who are interested in the technical underpinnings of Roche’s investigations to this end are referred to this 2013 publication by Roche and collaborators entitled Development and characterization of the cobas human papillomavirus test. In contrast to the tedious Pap test protocol and its “visually challenging” manual microscopic analysis, this “cobas”-based PCR test provided by Roche is fully automated.  The test process involves two instruments: one that completes sample preparation (COBAS® AmpliPrep) and another that performs the PCR process and detection of the pathogen DNA in real time (COBAS® TaqMan® Analyzer).

Incidentally, I traced-back the term “cobas” to late 1970’s Roche instrumentation named the “cobas-bio” analyzer, but could not decipher what “cobas” stands for! If any of you know the answer, please let us know by a comment at the end of this post.

FDA Panel Recommends Replacement for the Pap Test

This attention-grabbing headline of a March 2014 NY Times article by Andrew Pollock was the catalyst for my decision to research and write this blog exemplifying the “power of PCR” as a transformative diagnostic method. While this and numerous other popular news media all made reference to an FDA panel’s report, it took some digging to find the actual source-report, which is an 80-page pdf that can be accessed here to peruse in detail, if you wish. However, a much shorter but essential-fact-laden article by Joyce Frieden, News Editor of MedPage Today provided the following excerpts.

The FDA’s Medical Devices Advisory Committee Microbiology Panel agreed by a vote of 13-0 in each of three successive votes that the cobas® viral DNA test for HPV—made by Roche Molecular Systems—was safe and effective for cervical cancer screening, and that the benefits of the tests outweighed the risks. The Panel recommended that this Roche HPV test replace the Pap smear as the first-line standard of care for cancer screening.

The Roche test is seen as better than Pap tests in finding precancerous lesions (taken from the NY Times).

The Roche test is seen as better than Pap tests in finding precancerous lesions (taken from the NY Times)

The cobas® test currently has approval as a follow-up assessment for women 21 and older who have abnormal Pap tests, and as a co-test with the Pap smear to screen for the high-risk p16 and p18 HPV strains in women 30 to 65. The test comprises genotyping for HPV16 and 18 and pooled assessment of 12 additional high-risk HPV strains.

According to the proposal submitted by Roche, women 25 and older who test positive for HPV16 or 18 would proceed directly to colposcopy for further assessment.

Patients who test negative for HPV16 or 18 but positive for the other high-risk strains would have a Pap test to determine the need for colposcopy. Women who have a completely negative test would be followed at their physician’s discretion.

Panelists did express some concerns about dropping the age at which women should have the test from 30 to 25. The ATHENA study of over 47,000 patients with long-term follow-up used as the basis for the application found that about 11% of women ages 25 to 29 tested positive for HPV16 or 18 with the cobas test, compared with 7.28% among women 25 to 29 who had cytology alone as their first-line screening. Panel member Paula Hillard, MD, of Stanford University in California, was quoted as saying that would mean more patients in that age group “will be anxious about potentially having cancer.”

In addition, Hillard is quoted as expressing concern about off-label use. “I’m concerned that all those women potentially with other high-risk positivity won’t go to Paps next but go [straight] to colposcopy. That’s not what’s proposed here, but what control does FDA have once it’s out there?”

Panelist Kenneth Noller, MD, of the American Board of Obstetrics and Gynecology, in Dallas, agreed that real-world use could differ from the protocol proposed by Roche. He’s quoted as saying that “I’ve been watching how people practice; if you’re high-risk HPV positive you’re going to get colposcopy.” Furthermore, he said “that doesn’t necessarily mean it’s bad—it’s what you do with the colposcopy.”

Noller added that although he was “somewhat biased against dropping the age to 25 before I came here … I find the data presented today somewhat compelling to drop it to 25.”

Agreeing with this was panel member Kimberly Hanson, MD, MHS, of the University of Utah and ARUP Laboratories, both in Salt Lake City: “now we have the opportunity to identify women earlier, and to me that’s compelling,” adding that “although colposcopy is invasive and can be anxiety-provoking, it’s really very safe, so I think I’m leaning toward earlier screening.”

According to the summary submitted by FDA staff members, “The data show that the proposed primary screening indication for the cobas HPV test detects more women with disease and requires fewer women without disease to go to colposcopy than cytology alone.”

Benefit-risk analyses favored the HPV DNA test whether expressed in terms of number of cases of high-grade cervical disease per 10,000 women screened or per 100 colposcopy procedures.

The FDA is not bound to follow its advisory committees’ recommendations, but does so in most cases. On April 25—coincidentally DNA Day 2014—the FDA formally approved Roche’s HPV test as the First-Line Cervical Cancer Screening Method.

The “Entrenchment Factor”

At the risk of “throwing cold water” on the aforementioned PCR test benefits, I feel compelled to quote from Pollak’s NY Times story that ended with the following caveat.

“The Pap test, which is well entrenched and has been highly successful, will not go away quickly, if at all, however.

Assuming the FDA itself agrees with its advisory committee and approves the new use of Roche’s test, it would become just another option, not a replacement for the older testing regimens. And many doctors will not adopt the new test unless professional societies recommend it in guidelines, which could take years.”

Let’s all hope that these professional societies—and any other persuasive factors—lead to relatively rapid adoption by doctors.

As always, your comments are welcomed.

Venter’s Latest Venture: Increasing Human Longevity

  • The Quest to Make 100 the New 60
  • Aiming to Sequence 100,000 Human Genomes Per Year (Wow!)
  • Adding Genomes, Microbiomes, and Metabolomes to Health Records May Lead to Better Health and Longevity


Although this post is mainly about a new start-up called Human Longevity, whose mission is to apply genomics to guide increased longevity, the fact that this company was founded by J. Craig Venter has certainly created a “buzz.” The very name Venter—to me—is synonymous with scientifically unorthodox ideas that are big and bold. If you’re familiar with Venter’s accomplishments and “genomics rock star” status, go to the next section; if not, here are some highlights of his rise to fame.

As an investigator at NIH, Venter gained notoriety when he caused a brouhaha with his intentions to patent genes he discovered using expressed sequence tags (ESTs). The controversy was so extensive that it precipitated resignation of Nobel Laureate James D. Watson in 1992, who was then Director of NIH’s Human Genome Office. This caught the eye of a venture capitalist, Wallace Steinberg, who wanted to start a gene-finding company—with Venter as its head. Venter, however, insisted on a nonprofit venture, so Steinberg set him up in a nonprofit entity called The Institute for Genomic Research (TIGR) supported by a new company, Human Genome Sciences. (A NY Times story by Nicholas Wade entitled A Maverick Making Waves provides a nice overview of Venter’s career path through 2000).

Venter generated thousands of EST’s to the human genome that became the intellectual property of Human Genome Sciences and enabled the company to develop far-reaching claims to many medical genes of interest. In partnership with Nobel Laureate Hamilton O. Smith, Venter next used shotgun sequencing—then unproven, and controversial—to completely sequence Haemophilus influenzae. This gave scientists their first glimpse into the set of genes necessary for life. Moreover, this achievement set off a revolution in medical microbiology, inspiring efforts to decode every major pathogen and learn the microbes’ entire playbook for attacking human cells.

These early sequencing successes in turn led Michael W. Hunkapiller—then President of PE Biosystems, which made the leading brand of DNA sequencing instrument—to recruit Venter to run Celera—a new private company. Venter boldly declared to the media that Celera would decode the human genome using shotgun sequencing by 2001—ahead of the public consortium, sparking a contentious “race for the human genome.”

Fast forwarding from his role in decoding the human genome—described as the single most important scientific breakthrough of modern times—Venter is Founder, Chairman, and CEO of the J. Craig Venter Institute (JCVI), a non-profit research organization with approximately 300 scientists and staff dedicated to human, microbial, plant, synthetic and environmental genomic research, and the exploration of social and ethical issues in genomics.

Venter is also Founder and CEO of Synthetic Genomics Inc. (SGI), a privately held company dedicated to commercializing genomic-driven solutions to address global needs such as new sources of energy, new food and nutritional products, and next generation vaccines. Recently Venter announced his latest venture, Human Longevity Inc. (HLI), “a genomics and cell therapy-based diagnostic and therapeutic company focused on extending the healthy, high performance human life span.”

Venter relaxing on his 95-foot sailboat/research vessel named Sorcerer II.

Venter relaxing on his 95-foot sailboat/research vessel named Sorcerer II. Photograph: Rick Friedman/Corbis (taken from via Bing Images).

Since 2003, scientists at the J. Craig Venter Institute have been on a quest to unlock the secrets of the oceans by sampling, shotgun sequencing and analyzing the DNA of the microorganisms living in these waters. In February 2014, the vessel embarked on a sampling expedition of the Amazon River and its tributaries, which contains 1/5th of the Earth’s river flow.

Human Longevity: Genomics-Based Fountain of Youth?

The Fountain of Youth is a spring that supposedly restores the youth of anyone who drinks or bathes in its waters. Tales of such a fountain have been recounted across the world for thousands of years, beginning with writings by the Greek historian Herodotus. The tale was particularly prominent in the 16th century, when it became attached to the Spanish explorer Juan Ponce de León, who was searching for the Fountain of Youth when, in 1513, he traveled to what is now Florida.

Artistic rendering of Ponce de León accepting water from the Fountain of Youth (taken from via Bing Images).

Artistic rendering of Ponce de León accepting water from the Fountain of Youth (taken from via Bing Images).

Given this legendary history and our collective wish for healthy, long lives, it’s not surprising that Venter’s announcement earlier this year attracted widespread media attention and significant funding—to the tune of $70 million. A story in the NY Times refers to Venter as saying that the largest of the investors is K. T. Lim, a Malaysian billionaire who runs Genting Berhad, a gambling conglomerate. Venter adds that a ‘not insignificant’ part of the funding comes from Illumina—for reasons that will be appreciated by reading further.

The press release goes on to say that HLI’s funding is being used “to build the largest human sequencing operation in the world to compile the most comprehensive and complete human genotype, microbiome, and phenotype database available to tackle the diseases associated with aging-related human biological decline.” HLI is also “leading the development of cell-based therapeutics to address age-related decline in endogenous stem cell function.”

In addition, HLI’s “revenue streams will be derived from database licensing to pharmaceutical, biotechnology and academic organizations, sequencing, and development of advanced diagnostics and therapeutics.”

Venter is quoted as saying that “using the combined power of our core areas of expertise—genomics, informatics, and stem cell therapies, we are tackling one of the greatest medical/scientific and societal challenges—aging and aging related diseases,” and that “HLI is going to change the way medicine is practiced by helping to shift to a more preventive, genomic-based medicine model which we believe will lower healthcare costs. Our goal is not necessarily lengthening life, but extending a healthier, high performing, more productive life span.”

HLI cofounder Peter H. Diamandis, M.D. puts this another and trendier way, according to the NY Times, which quotes Diamandis as saying that the goal was not to make people live forever, but rather to make “100 years old the next 60.” The NY Times goes on to say that “Venter, who is 67, sounds as if he might not need the company to succeed. Quoting Venter, “I feel like I have at least 20 or 30 years left in my career.”

HLI’s humongous database-to-be will surely be, in my opinion, a prime example of Big Data—itself a “hot trend.” It aims to have genomic sequences from “a variety of humans—children, adults and super centenarians [i.e. people who have attained the age of at least 110 years] and those with disease and those that are healthy,” according to the press release.

Illumina Looms Large in Longevity’s Plans

HLI has initially purchased two Illumina HiSeq X Ten Sequencing Systems (with the option to acquire three additional systems) to sequence up to 40,000 human genomes per year, with plans to rapidly scale to 100,000 human genomes per year.

Let me repeat this to be sure you don’t think these are typos.

40,000 and then 100,000 human genomes per year!

As pictured below, each of these newly introduced Sequencing Systems is comprised of ten—count them—instruments, which I’ve previously written about as enabling the long-elusive $1,000 genome cost target. Ironically, this goal was set by Venter as a technical challenge in 2002 at a now monumental TIGR conference.

Each Illumina HiSeq X Ten Sequencing System has a list price of $10 million.

Each Illumina HiSeq X Ten Sequencing System has a list price of $10 million.

Microbiome and Metabolome Data

Relative proportion of sequences determined at the taxonomic phylum level at eight anatomical sites. High-throughput sequencing has revealed substantial intra-individual microbiome variation at different anatomical sites, and inter-individual variation at the same anatomical sites. Such site-specific differences and the observed conservation between human hosts provide an important framework to determine the biological and pathological significance of a particular microbiome composition (taken from via Bing Images).

Relative proportion of sequences determined at the taxonomic phylum level at eight anatomical sites. High-throughput sequencing has revealed substantial intra-individual microbiome variation at different anatomical sites, and inter-individual variation at the same anatomical sites. Such site-specific differences and the observed conservation between human hosts provide an important framework to determine the biological and pathological significance of a particular microbiome composition (taken from via Bing Images).

Along with the genomic data gleaned from the sequencing of complete human genomes, HLI will also be generating microbiome data for many of these individuals through its Biome Healthcare division. The division is lead by Karen Nelson, who at TIGR led the first human microbiome study on the human gut published in Science in 2006.

The microbiome— a very “hot” trend in genomics research that I wrote about last year—consists of all the microbes that live in and on the human body that contribute to health and disease status of an individual. By better understanding a person’s microbiome—from gut, oral, skin, lung, and other body sites—the company said that it “anticipates developing improved probiotics and other advanced diagnostic and therapeutic approaches to improve health and wellness.”

HLI will also capture and analyze each individual’s metabolomic data. The metabolome is the full complement of metabolites, biochemicals and lipids circulating throughout the human body. HLI has signed an agreement with Metabolon Inc., a diagnostic products and services company offering a biochemical profiling platform, to capture this information from each of the genomic samples that HLI is collecting. “Metabolomics is important because quantifying and understanding the full picture of circulating chemicals in the body can help researchers get a clearer picture of that individual’s health status, and provide markers and pathways associated with drug action,” according to HLI.

Schematic of the 'omic hierarchy: genomics, transcriptomics, proteomics, and metabolomics—yes, the figure leaves out a few others, e.g. epigenomics and phenomics (taken from via Bing Images).

Schematic of the ‘omic hierarchy: genomics, transcriptomics, proteomics, and metabolomics—yes, the figure leaves out a few others, e.g. epigenomics and phenomics (taken from via Bing Images).

Stem Cell Therapies

This part of the company’s multi-pronged strategy utilizing stem cell therapy advances is said to be “premised on the theory that as the human body ages many biological changes occur, including substantial changes and degradation to the genome of the differentiated, specialized cells found in all body tissues. There is also a depletion and degradation of healthy regenerative stem cell populations in the body over time. HLI will monitor the genomic changes which occur during stem cell differentiation, normal aging, and in association with the onset of disease.”

In this regard, it’s worth mentioning that TriLink BioTechnologies is a leading provider of biosynthetic modified mRNAs that encode factors used for cellular reprograming and regenerative medicine. Further information about these catalog products and custom services is available here.

Commercial Potential

Robert Hariri, M.D., Ph.D., who cofounded HLI with Venter and Diamandis, is quoted in HLI’s press release as saying that “the global market for healthy human longevity is enormous with total healthcare expenditures in those 65 and older running well over $7 trillion.” He adds, “we believe that HLI’s unique science and technology, along with our business leadership, will positively impact the healthcare market with novel diagnostics and therapeutics.”

Time will tell.

Personally, over the many years since Mike Hunkapiller introduced me to then “NIHer” Craig Venter, I’ve learned not to bet against him.

In closing, I should mention that Venter et al. are not the first to eye the commercial potential of longevity. Last September, Google’s chief executive, Larry Page, announced that his company was creating an anti-aging company, Calico, which is being run by Arthur D. Levinson, the former chief executive of Genentech. Even earlier, Oracle’s chief executive, Lawrence J. Ellison, had financed anti-aging research through his foundation. However, last December, Ellison announced this research would end due to a funding crunch.

Your comments are welcomed.

Smartphone Science: Nifty Accessories for Bio-Medical Applications

  • DIY Cholesterol and Vitamin D Monitoring Using Smartphones
  • Single-molecule Microscopy on Smartphones…Coming Soon?
  • Pee-powered Smartphones Developed
  • Solar Powered Smartphone-assisted “sample-to-answer” with PCR and Human Skin Biopsies Demonstrated


It’s hard to believe that the first cell phone (invented about 30 years ago) was actually considered to be very convenient even though it weighed more than two pounds and looked like a large brick—plus it took 10 hours to charge the battery to get only 30 minutes of talk-time—“o BTW no txt” back then, either! Fortunately, that cell phone has evolved into present day smartphones, which are amazingly versatile and seemingly ubiquitous extensions of our hands, thumbs, mouths, and minds that can talk to us and remind us what to do. 

Motorola produced the first handheld mobile phone (far left). Martin Cooper, a Motorola engineer and executive, made the first mobile telephone call from handheld subscriber equipment on April 3, 1973 in front of reporters, placing a call to Dr. Joel S. Engel of Bell Labs. Cooper has stated his vision for the handheld device was inspired by Captain James T. Kirk using his Communicator (far right) in the 1960s television show Star Trek.

Motorola produced the first handheld mobile phone (far left). Martin Cooper, a Motorola engineer and executive, made the first mobile telephone call from handheld subscriber equipment on April 3, 1973 in front of reporters, placing a call to Dr. Joel S. Engel of Bell Labs. Cooper has stated his vision for the handheld device was inspired by Captain James T. Kirk using his Communicator (far right) in the 1960s television show Star Trek.

Evolution of Smartphones

Present day smartphones are essentially hand-held computers with lots of processing speed and memory that allow us to communicate in various ways, take remarkably high-quality digital pictures, “surf the net”, have docking ports, and can run hundreds of thousands of applications. Given their impressive functionality and remarkable convenience, it’s not surprising that there is increasing interest in developing plug-in accessories to enable smartphones to carryout various types of bio-medical applications.

One of my previous posts highlighted a report of DNA isothermal amplification/fluorescence detection using a disposable microchip interfaced with an iPod Touch—and transmitting the results via a WiFi interface—as an example of the trend toward point-of-care (POC) and even self-diagnostic tools. Following are a few recent examples that further illustrate this trend employing smartphones.

Testing Cholesterol and Vitamin D Levels with Your Smart Phone

It is estimated that 60% of adults in the US have high cholesterol (>200 mg/dL), and 37 million have very high cholesterol (>250 mg/dL). Studies on the effect of serum cholesterol on coronary heart disease mortality indicate that there is a 17% increase in mortality for every 20 mg/dL increase above 210 mg/dL, but often time high cholesterol goes undetected.

Earlier this year, a team of US scientists reported that they had developed a smartphone accessory that will allow individuals to test their blood cholesterol levels themselves. Self-detection and routine monitoring would undoubtedly save lives given that cholesterol levels can often be controlled through simple changes in diet such as consuming less saturated fat.

Prof. David Erickson using his iPhone interfaced with a blood test strip. Photo credit: Jason Koski/University Photography; taken from via Bing Images.

Prof. David Erickson using his iPhone interfaced with a blood test strip. Photo credit: Jason Koski/University Photography; taken from via Bing Images.

Prof. David Erickson and co-workers from Cornell University in New York developed a system that consists of a small accessory device that attaches onto a smartphone, an app, and dry reagent test strips that are already commercially available. A drop of blood is placed onto the test strip and an enzymatic, colorimetric reaction occurs. This strip is then placed into the accessory device and an image of the strip is generated using the camera on the phone. The app then quantifies the color change and converts this into a blood cholesterol concentration using a calibration curve. Check out this “must see” video of Prof. Erickson demonstrating how it all works.

According to Megan Tyler reporting in Chemistry World, the achievement of Erickson and his colleagues should not be understated. Although what they have done may sound simple, developing a smartphone-based system that enables precise and reproducible diagnostic measurements is actually very difficult. She adds that “the largest challenge comes from having to account for different lighting conditions and reaction times, differences between the cameras and camera settings in different types of phone, and the potential for misalignment of the test strip.” The team overcame the lighting problem by using the accessory device to block out external light so that the test strip would be uniformly illuminated by the flash on the camera. Meanwhile, algorithms in the app account for the other potential variables.

Tyler reports that Erickson and co-workers are now working to commercialize their system, so it may be available for the general public to purchase in the near future.

I contacted Prof. Erickson to obtain a copy of his publication about this system (called  “smartCARD”—smartphone Cholesterol Application for Rapid Diagnostics) so I could read about the details.

Read about low, normal, and high levels of HDL, LDL, triglycerides and cholesterol at Understanding Cholesterol (taken from via Bing Images).

Read about low, normal, and high levels of HDL, LDL, triglycerides and cholesterol at Understanding Cholesterol (taken from via Bing Images).

In that paper, he concludes by stating that “…using the smartCARD system presented here it is possible to measure other commercially available colorimetric test strips for LDL, HDL, cholesterol, and triglycerides. Such a device would be a great advance in “cloud” based self-diagnostics and monitoring of this quartet of compounds critical to our cardiovascular health.

As I was finishing this blog, I came across yet another publication led by Prof. Erickson entitled “A smartphone platform for the quantification of vitamin D levels.” The abstract begins with pointing out that Vitamin D deficiency has been linked to a number of diseases and adverse outcomes including: osteoporosis, infections, diabetes, cardiovascular diseases, and even cancer. At present the vast majority of vitamin D testing is performed in large-scale laboratories at the request of a physician as part of an annual panel of blood tests. In contrast, Erickson and coworkers developed a DIY system for rapid quantification of vitamin D using a system similar to the cholesterol test decribed above that enables colorimetric detection of Vitamin D using a novel gold nanoparticle-based immunoassay. This system was compared with well-established ELISA test kits for serum samples of unknown concentration, and gave equivalency of the results. These investigators concluded that they “envision this as the first step towards the development of the NutriPhone, a comprehensive system for the analysis of multiple vitamins and micronutrients on a smartphone.”

Single-molecule Microscopy on a Smartphone…Coming Soon?

Lord Kelvin—17th century inventor of the eponymous Kelvin temperature scale and source of provocative quotes—helped calculate Avogadro’s number, one I know all too well from my days working in the lab with seemingly very tiny quantities of material, such as picomoles of oligonucleotide primers for PCR. Looking back, the number of oligonucleotide molecules was still quite large, 6.022 x 1011, thus I’ve been mightily impressed—if not downright amazed—by the trend in new technologies for manipulating and optically detecting single molecules, let alone doing this using a smartphone!

Taken from via Bing Images

Taken from via Bing Images

Aydogan Ozcan received the 2011 Presidential Early Career Award for Scientists and Engineers (taken from via Bing Images).

Aydogan Ozcan received the 2011 Presidential Early Career Award for Scientists and Engineers (taken from via Bing Images).

Single-molecule optical detection on a smartphone would be truly amazing because it would need to enable technical achievements that usually require big, powerful lasers and large microscopes that take up lots of bench space and operate in a pitch-black lab. A major step toward this seemingly impossible goal has received considerable editorial praise in ACS Nano—a premier specialty journal of the American Chemical Society—as well as widespread science media coverage. The team at UCLA that’s getting all this well-deserved attention is led by Prof. Aydogan Ozcan, whom I wrote about here last year as “adapting smartphones for measurement of the cell count of HIV patients in resource limited settings or doing fluorescent microscopy.”

According to the UCLA Newsroom, your smartphone now can see what the naked eye cannot: a single virus less than one-thousandth of the width of a human hair. Prof. Ozcan’s team have created a portable smartphone attachment that can be used to perform sophisticated field testing to detect viruses and bacteria without the need for bulky and expensive microscopes and lab equipment. The device weighs less than half a pound.

“This cellphone-based imaging platform could be used for specific and sensitive detection of sub-wavelength objects, including bacteria and viruses and therefore could enable the practice of nanotechnology and biomedical testing in field settings and even in remote and resource-limited environments,” Ozcan said. “These results also constitute the first time that single nanoparticles and viruses have been detected using a cellphone-based, field-portable imaging system.”

The new research, published in ACS Nano, comes on the heels of Ozcan’s other recent inventions, including a cellphone camera–enabled sensor for allergens in food products and a smart phone attachment that can conduct common kidney tests.

Capturing clear images of objects as tiny as a single virus is difficult because the optical signal strength and contrast are very low for objects that are smaller than the wavelength of light. In the ACS Nano paper, Ozcan details a fluorescent microscope device fabricated by 3D printing—a very hot trend in science, and consumer products—that contains a color filter, an external lens and a laser diode. As pictured here, the diode illuminates fluid or solid samples at a steep angle of roughly 75 degrees. This oblique illumination avoids detection of scattered light that would otherwise interfere with the intended fluorescent image.

Using this device attached to the camera module on a smartphone, Ozcan’s team was able to detect single human cytomegalovirus (HCMV) particles. HCMV is a common virus that can cause birth defects such as deafness and brain damage. This same virus can hasten the death of adults who have received organ implants, who are infected with the HIV virus or whose immune systems have otherwise been weakened. A single HCMV particle measures about 150–300 nanometers; a human hair is roughly 100,000 nanometers thick. To verify these results, researchers in Ozcan’s lab used a photon-counting confocal microscope.

(a) Cell phone image of fluorescently labeled HCMV at a concentration of 107 PFU/mL. (b) Photon-counting map for dashed area in (a) using a confocal laser microscope. Note that absolute photon counts are different. (c) Distribution of intensity of HCMV in cell phone images. (d) Cell-phone-based virus density vs. virus incubation concentrations [taken from Wei et al. ACS Nano (2013)].

(a) Cell phone image of fluorescently labeled HCMV at a concentration of 107 PFU/mL. (b) Photon-counting map for dashed area in (a) using a confocal laser microscope. Note that absolute photon counts are different. (c) Distribution of intensity of HCMV in cell phone images. (d) Cell-phone-based virus density vs. virus incubation concentrations [taken from Wei et al. ACS Nano (2013)].

It’s important to note that these feasibility studies used Alexa-488-conjugated secondary antibody to multiply label HCMV via an abundant glycoprotein molecule, which was the target of a first antibody. Thus a single virus has many fluorophores thereby increasing detection sensitivity. The Editorial in ACS Nano suggests that the ultimate goal of imaging any unlabeled virus (or other microbe) might be achieved by hybridization with genome specific, doubly labeled oligonucleotides called molecular beacons (available from TriLink, I might add) that “light up” only after binding to the genomic target, as shown in Figure 1 below.

Taken from Khatua & Orrit, ACS Nano (2013).

Taken from Khatua & Orrit, ACS Nano (2013).

Hopefully, Prof. Ozcan’s vision of a smartphone-based “field-portable imaging system” will become a reality in the near future. If so, this raises the challenging issue of having adequate battery power for the smartphone. Solar-based battery charging stations are one solution, but what if the sun doesn’t cooperate when needed? The next section describes an alternative approach that—in my opinion—is quite creative, to say the least.

“Pee Powered” Smartphones

As reported by Jennifer Newton in Chemistry World, the first cell phone battery to be directly charged by microbial fuel cells feeding on urine has been described by scientists in the UK. This work builds upon previous experiments in 2011 aimed at development of urine-powered fuel cells by Loannis Leropoulos and colleagues at Bristol Robotics Laboratory. They had shown that urine was an excellent fuel for direct electricity generation. As a bonus, the cells can reclaim essential nutrients from the urine, making wastewater treatment easier.

urineThis latest study is the first time a commercially available mobile phone has been powered by urine-powered fuel cells. Cascades of electrically connected fuel cells use bacterial action to convert chemical energy in organic matter in urine into electricity.

The team hopes their work will lead to emergency charging devices for remote locations. The diagram below illustrates one embodiment. Some field conditions might require alternative—dare I say primitive—means of collecting urine, as well as easily portable fuel cells.

If you’ve been exploring the diagnostic potential of smartphones or, shall we say, organic ways of powering these phones, we’d be most interested in hearing from you via the comments section below. As always, all thoughts and opinions are welcomed.


After completing this post, Prof. Erickson’s group published a proof-of-concept study of a solar powered, smartphone-assisted “sample-to-answer” molecular diagnostic test with PCR and human skin biopsies. The following are key aspects of the abstract from Nature:

“Here we integrate solar heating with microfluidics to eliminate thermal cycling power requirements as well as create a simple device infrastructure for PCR. Tests are completed in less than 30 min, and power consumption is reduced to 80 mW, enabling a standard 5.5 Wh iPhone battery to provide 70 h of power to this system. Additionally, we demonstrate a complete sample-to-answer diagnostic strategy by analyzing human skin biopsies infected with Kaposi’s Sarcoma herpesvirus through the combination of solar thermal PCR, HotSHOT DNA extraction and smartphone-based fluorescence detection. We believe that exploiting the ubiquity of solar thermal energy as demonstrated here could facilitate broad availability of nucleic acid-based diagnostics in resource-limited areas.”