1) The document discusses the development of a molecular diagnostic technique called smaRT-LAMP that can detect pathogens like Salmonella Typhimurium in blood using a smartphone. 2) The technique was able to detect Trypanosoma cruzi, the causative agent of Chagas disease, in whole blood at concentrations fourfold below clinical levels for 1/500th of the cost of standard PCR. 3) Further development led to a system called smaRT-LAMP that can quantitatively detect Salmonella Typhimurium in real-time using isothermal amplification on a smartphone via an app. It was tested on mice and confirmed infections levels associated with sepsis.

1. Office of Research – California NanoSystems Institute
A Research Statement
By Faye Walker, Ph.D. |OCTOBER 24, 2016
An Introduction: Molecular Diagnostics
I work with the backbone of life: deoxyribonucleic acid, or DNA. The messages encoded in
nucleic acids form our traits, tendencies, and sense of self. But DNA and RNA (ribonucleic
acid) explain more than our state of health. They explain, on a basic chemical level, the
form and function of disease.
Today, scientific advancements in healthcare have become reliant on genomics, genetics,
and other DNA-based studies. With the ability to distinguish molecular targets at the level
of their genome, medical practitioners have gained the ability to identify pathogens
according to their species, subspecies, and strain. Such specificity is essential for ensuring
that healthcare strikes the correct target in terms of medications, dosages, and follow-up
treatments.
This level of specificity could seriously impact our management of infectious diseases.
Once, antibiotics like penicillin were a cure-all for microbial infections. Now, an increasing
number of microorganisms exhibit resistance to common medications. The difference
between a methicillin-susceptible strain of Staphylococcus aureus and a methicillin-
resistant one could mean the difference between life and death.
Specific disease diagnostics can cut risks for patients and prevent infection from spreading.
But knowing the cause of an illness is only one key factor in treating patients. Another is
timing. Speed is critical for linking proper treatment to recovery. Physicians are faced with
the task of screening for harmful behaviors, substances, and organisms to implement a
course of action. If they aren’t finished within minutes, it might be too late.
So if clinicians are fighting the clock with their own two hands, how can they win? My idea
was to put the right tools into their hands. More accurately, to use the tools that they
already have at-hand: smartphones.
Phones take a primary position in my research with nucleic acid amplification tests. They
are used for both recording and interpreting the results of a DNA amplification assay.
Implementing the tests themselves is as easy as downloading an app, giving anyone with
an internet connection the ability to test for causative agents of disease.
A Recap: Preliminary Results
Under Prof. H. Tom Soh, I worked with Kareem Ahmad to create a practical, low-cost
method for performing nucleic acid tests. Each test required only a small pinprick of blood.
The blood was then combined with a pre-mixed set of reagents and placed within a
computer for a polymerase chain reaction (PCR). PCR relies on increasing and decreasing
the temperature of the mixture in order to amplify target DNA. At the lower temperature, the
polymerase recognizes a specific sequence of DNA. The enzyme can then create more
copies of this sequence. Raising the temperature releases the polymerase and readies the
target DNA to be used again, resulting in an exponential rate of amplification.

2. I used the PC-PCR-Phone (P3) system to detect genomic DNA from the causative agent of
Chagas disease, Trypanosoma cruzi, in whole blood at concentrations fourfold below the
average clinical load. From beginning to end, from computer to phone costs, the entire
process could be done for 1/500th
of the price of a standard laboratory PCR setup. It meant
success. It meant bringing together the worlds of research development and real-world
practicality. It meant making mobile healthcare possible in low-resource settings that
lacked the infrastructure of fully-equipped and staffed clinical research laboratories.
So I worked further towards developing technology that would be suitable for users at the
point-of-care. With the help of scientists in Prof. Michael Mahan’s laboratory and an app
developer at SONOS, Inc., I developed a platform capable of quantitatively measuring
Salmonella enterica serovar Typhimurium in whole blood.
This project moved above and beyond the previous one. First, it made use of continuous,
real-time data collection and processing. Monitoring DNA amplification in real-time reduces
operator error and increases quantitative accuracy for very precise, reproducible results.
Second, the DNA amplification reaction was isothermal. Loop-mediated isothermal
amplification, or LAMP, is an up-and-coming technology that relies on an autocycling
polymerase. No temperature cycling is needed; the enzyme itself has the ability to fold,
amplify, and unfold DNA for an exponential increase in the amount of target.
All in all, the design of the smaRT-LAMP (smartphone Real Time-Loop mediated isothermal
AMPlification) system required no manufacture and was freely available via an Android app.
It was a marriage of something available and something technical. And with all the
components in place, it achieved results.
I put the smaRT-LAMP platform to the test with real samples. At the late stage of sepsis,
mice infected with Salmonella Typhimurium should exhibit high levels of the pathogen in
their blood. Using smaRT-LAMP for all steps of blood collection, sample loading, and DNA
quantification, the results confirmed that the infected animals showed at least 104
colony-
forming units of bacteria per milliliter of blood. In clinical terms, this meant certain death. In
experimental terms, it meant that we had a way to prevent such deaths by early detection.
A Vision: Upcoming Research
Preventative care is my end goal in research. By and large, medicine is moving more
towards healthcare in the truest sense of the word: caring for health. Sick-care has long
been the norm. As a society, we react to our physical problems rather than proactively
maintaining a fit status. Making diagnostics technology more readily available can pave the
way to facilitate this positive change in medicine.
Rapid, robust, and user-friendly technology has potential near and far, in the long-term and
short-term. I plan to apply my smaRT-LAMP setup to disease diagnostics with
Streptococcus pneumonia, Yersinia pseudotuberculosis, and Staphylococcus aureus. I
want to modify it to work on multiple samples, from blood to urine to skin swabs.
Practically, what I most want is for smaRT-LAMP to be adopted as a clinical tool. I want to
facilitate its introduction by streamlining the equipment requirements for its performance.
With a 3-D printer, a single apparatus could be mass-produced and distributed; with
lyophilization and proper packaging, reagents could be distributed without the need for
refrigeration. I hope that in pursuing these goals, I can do my part to help save lives.