Transformation of personal computers and mobile phones into genetic diagnostic systems

Development of an equipment free paper based fluorimetric method for the selective determination of histidine in human urine samples

A direct fluorimetric method, employing μicro-analytical paper-based devices (μ-PADs) for the selective determination of histidine (HIS) is described. The suggested method exploits the fluorescence emission of histidine after its rapid reaction with o-phthalaldehyde (OPA) at a basic medium (pH = 10) on the surface of a paper device with the application of a UV lamp at 354 nm. The devices are inexpensive and are composed of chromatographic paper and wax barriers. The analytical protocol is easily applicable with minimal technical expertise and without the need of expensive experimental apparatus. The user has to add a test sample, illuminate the device with a UV lamp, and read the fluorescence of the sensing area using a simple imaging device such as a cell-phone camera. The method is free from common interferences likely to affect the measurement of histidine and is selective among all other amino acids. This analytical procedure was optimized and validated, paying special attention to its intended application. The detection limits are as low as 1.8 μM with very satisfactory precision ranging from 6.4% (intra-day) to 8.9% (inter-day). Random urine samples from adult volunteers (n = 5) were successfully analyzed and HIS content ranged between 260 and 1114 μmol L^-1 with percentage recoveries in the range of 78.2 and 124.6%.

Advances in Directly Amplifying Nucleic Acids from Complex Samples

Advances in nucleic acid amplification technologies have revolutionized diagnostics for systemic, inherited, and infectious diseases. Current assays and platforms, however, often require lengthy experimental procedures and multiple instruments to remove contaminants and inhibitors from clinically-relevant, complex samples. This requirement of sample preparation has been a bottleneck for using nucleic acid amplification tests (NAATs) at the point of care (POC), though advances in “lab-on-chip” platforms that integrate sample preparation and NAATs have made great strides in this space. Alternatively, direct NAATs—techniques that minimize or even bypass sample preparation—present promising strategies for developing POC diagnostic tools for analyzing real-world samples. In this review, we discuss the current status of direct NAATs. Specifically, we surveyed potential testing systems published from 1989 to 2017, and analyzed their performances in terms of robustness, sensitivity, clinical relevance, and suitability for POC diagnostics. We introduce bubble plots to facilitate our analysis, as bubble plots enable effective visualization of the performances of these direct NAATs. Through our review, we hope to initiate an in-depth examination of direct NAATs and their potential for realizing POC diagnostics, and ultimately transformative technologies that can further enhance healthcare.

Consumer electronics devices for DNA genotyping based on loop-mediated isothermal amplification and array hybridisation

Consumer electronic technologies offer practical performances to develop compact biosensing systems intended for the point-of-care testing of DNA biomarkers. Herein a discrimination method for detecting single nucleotide polymorphisms, based on isothermal amplification and on-chip hybridisation, was developed and integrated into user-friendly optical devices: e.g., USB digital microscope, flatbed scanner, smartphone and DVD drive. In order to adequately identify a single base change, loop-mediated isothermal amplification (LAMP) was employed, with high yields (8 orders) within 45 min. Subsequently, products were directly hybridised to the allele-specific probes attached to plastic chips in an array format. After colorimetric staining, four consumer electronic techniques were compared. Sensitive precise measurements were taken (high signal-to-noise ratios, 10-μm image resolution, 99% scan-to-scan reproducibility). These features confirmed their potential as analytical tools, are a competitive alternative to fluorescence scanners, and incorporate additional advantages, such as user-friendly interface and connectivity for telemedicine needs. The analytical performances of the integrated platform (assay and reader) in the human samples were also excellent, with a low detection limit (100 genomic DNA copies), and reproducible (<15%) and cheap assays (< 10 €/test). The correct genotyping of a genetic biomarker (single-nucleotide polymorphism located in the GRIK4 gene) was achieved as the assigned genotypes agreed with those determined by using sequencing. The portability, favourable discriminating and read-out capabilities reveal that the implementation of mass-produced low-cost devices into minimal-specialised clinical laboratories is closer to becoming a reality.

Portable Spectroscopy

Until very recently, handheld spectrometers were the domain of major analytical and security instrument companies, with turnkey analyzers using spectroscopic techniques from X-ray fluorescence (XRF) for elemental analysis (metals), to Raman, mid-infrared, and near-infrared (NIR) for molecular analysis (mostly organics). However, the past few years have seen rapid changes in this landscape with the introduction of handheld laser-induced breakdown spectroscopy (LIBS), smartphone spectroscopy focusing on medical diagnostics for low-resource areas, commercial engines that a variety of companies can build up into products, hyphenated or dual technology instruments, low-cost visible-shortwave NIR instruments selling directly to the public, and, most recently, portable hyperspectral imaging instruments. Successful handheld instruments are designed to give answers to non-scientist operators; therefore, their developers have put extensive resources into reliable identification algorithms, spectroscopic libraries or databases, and qualitative and quantitative calibrations. As spectroscopic instruments become smaller and lower cost, "engines" have emerged, leading to the possibility of being incorporated in consumer devices and smart appliances, part of the Internet of Things (IOT). This review outlines the technologies used in portable spectroscopy, discusses their applications, both qualitative and quantitative, and how instrument developers and vendors have approached giving actionable answers to non-scientists. It outlines concerns on crowdsourced data, especially for heterogeneous samples, and finally looks towards the future in areas like IOT, emerging technologies for instruments, and portable hyphenated and hyperspectral instruments.

"Smart Diagnosis" of Parasitic Diseases by Use of Smartphones

Accurate and rapid diagnosis is crucial in combating parasitic diseases that cause millions of deaths worldwide. However, the scarcity of specialized diagnostic equipment in low- and middle-income countries is one of the barriers to effective management of parasitic diseases and warrants the need for alternative, inexpensive, point-of-care diagnostic tools. Due to their multiple built-in sensors, smartphones offer cost-effective alternative to expensive diagnostic devices. However, the use of smartphones in parasitic diagnoses remains in its infancy. This minireview describes various smartphone-based devices applied specifically for the diagnosis of parasitic diseases and discusses challenges and potential implications for their use in future.

A smart device application for the automated determination of E. coli colonies on agar plates

The manual counting of colonies on agar plates to estimate the number of viable organisms (so-called colony-forming units-CFUs) in a defined sample is a commonly used method in microbiological laboratories. The automation of this arduous and time-consuming process through benchtop devices with integrated image processing capability addresses the need for faster and higher sample throughput and more accuracy. While benchtop colony counter solutions are often bulky and expensive, we investigated a cost-effective way to automate the colony counting process with smart devices using their inbuilt camera features and a server-based image processing algorithm. The performance of the developed solution is compared to a commercially available smartphone colony counter app and the manual counts of two scientists trained in biological experiments. The comparisons show a high accuracy of the presented system and demonstrate the potential of smart devices to displace well-established laboratory equipment.

Molecular diagnostics for Chagas disease: up to date and novel methodologies

INTRODUCTION

Chagas disease is caused by the parasite Trypanosoma cruzi. It affects 7 million people, mainly in Latin America. Diagnosis is usually made serologically, but at some clinical scenarios serology cannot be used. Then, molecular detection is required for early detection of congenital transmission, treatment response follow up, and diagnosis of immune-suppression reactivation. However, present tests are technically demanding and require well-equipped laboratories which make them unfeasible in low-resources endemic regions. Areas covered: Available molecular tools for detection of T. cruzi DNA, paying particular attention to quantitative PCR protocols, and to the latest developments of user-friendly molecular diagnostic methodologies. Expert commentary: In the absence of appropriate biomarkers, molecular diagnosis is the only option for the assessment of treatment response. Besides, it is very useful for the early detection of acute infections, like congenital cases. Since current Chagas disease molecular tests are restricted to referential labs, research efforts must focus in the implementation of easy-to-use diagnostic tools in order to overcome the access to diagnosis gap.

Low-cost colorimetric assay of biothiols based on the photochemical reduction of silver halides and consumer electronic imaging devices

This work describes a new approach for the determination of free biothiols in biological fluids that exploits some of the basic principles of early photographic chemistry - that was based on silver-halide recording materials - and uses broadly-available imaging devices (i.e. flatbed scanners) as detectors. Specifically, the proposed approach relies on the ability of biothiols to bind to silver ions and dissociate the silver halide crystals thus changing the photosensitivity of silver halide crystal suspension. The changes induced by biothiols on the light intensity transmitted through the silver halide suspension, after photochemical reduction, were measured with a simplified photometric approach that employs a flatbed scanner operating in transmittance mode. The overall analytical procedure for the determination of biothiols was easily executable, fast and could be applied with inexpensive and commercially available materials and reagents. What is more, physiologically relevant biothiol levels could be inspected even by the unattended eye. The developed assay was successfully applied to the determination of biothiols in urine and blood plasma samples with detection limits as low as 10μM, satisfactory recoveries (92-97%), good reproducibility (6.7-8.8%) and high selectivity against other major components of biological fluids. The utility of the method to the determination of reduced/oxidized thiol ratio's as well as its application under natural light illumination, without external energy sources, was also demonstrated and is discussed with regard to point-of need applications in facility-limited settings.

Wireless Data Acquisition of Transient Signals for Mobile Spectrometry Applications

Wireless data acquisition using smartphones or handhelds offers increased mobility, it provides reduced size and weight, it has low electrical power requirements, and (in some cases) it has an ability to access the internet. Thus, it is well suited for mobile spectrometry applications using miniaturized, field-portable spectrometers, or detectors for chemical analysis in the field (i.e., on-site). There are four main wireless communications standards that can be used for wireless data acquisition, namely ZigBee, Bluetooth, Wi-Fi, and UWB (ultra-wide band). These are briefly reviewed and are evaluated for applicability to data acquisition of transient signals (i.e., time-domain) in the field (i.e., on-site) from a miniaturized, field-portable photomultiplier tube detector and from a photodiode array detector installed in a miniaturized, field-portable fiber optic spectrometer. These are two of the most widely used detectors for optical measurements in the ultraviolet-visible range of the spectrum. A miniaturized, 3D-printed, battery-operated microplasma-on-a-chip was used for generation of transient optical emission signals. Elemental analysis from liquid microsamples, a microplasma, and a handheld or a smartphone will be used as examples. Development and potential applicability of wireless data acquisition of transient optical emission signals for taking part of the lab to the sample types of mobile, field-portable spectrometry applications will be discussed. The examples presented are drawn from past and ongoing work in the authors' laboratory. A handheld or a smartphone were used as the mobile computing devices of choice.

A Rapid and Low-Cost PCR Thermal Cycler for Infectious Disease Diagnostics

The ability to make rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a great step forward in global health. Many molecular diagnostic assays are developed based on using thermal cyclers to carry out polymerase chain reaction (PCR) and reverse-transcription PCR for DNA and RNA amplification and detection, respectively. Unfortunately, most commercial thermal cyclers are expensive and need continuous electrical power supply, so they are not suitable for uses in low-resource settings. We have previously reported a low-cost and simple approach to amplify DNA using vacuum insulated stainless steel thermoses food cans, which we have named it thermos thermal cycler or TTC. Here, we describe the use of an improved set up to enable the detection of viral RNA targets by reverse-transcription PCR (RT-PCR), thus expanding the TTC's ability to identify highly infectious, RNA virus-based diseases in low resource settings. The TTC was successful in demonstrating high-speed and sensitive detection of DNA or RNA targets of sexually transmitted diseases, HIV/AIDS, Ebola hemorrhagic fever, and dengue fever. Our innovative TTC costs less than $200 to build and has a capacity of at least eight tubes. In terms of speed, the TTC's performance exceeded that of commercial thermal cyclers tested. When coupled with low-cost endpoint detection technologies such as nucleic acid lateral-flow assay or a cell-phone-based fluorescence detector, the TTC will increase the availability of on-site molecular diagnostics in low-resource settings.

Rapid infectious diseases diagnostics using Smartphones

The "Smartphone" is an almost universal possession in high-income populations, and is rapidly becoming so in lower-income regions, particularly among urban populations, and serves social networking and a quest for information and knowledge. The field of infectious disease diagnostics is at a potential watershed moment, with the essential building blocks for the development of diagnostic assays being ever more available and affordable, which is leading to creative innovative approaches to developing much-needed accurate and simple point-of-care (POC) diagnostic tools for high disease burden, low-income settings. We review the importance and implications of a paper published in Science Translational Medicine on the development of a smartphone-powered and -controlled multiplex immunological assay that tests for HIV and syphilis simultaneously. This is reviewed in the context of other prototype smartphone-enabled/assisted diagnostic devices, and how such developments might shape the future of the POC diagnostics field.

Integrated Microfluidic Nucleic Acid Isolation, Isothermal Amplification, and Amplicon Quantification

Microfluidic components and systems for rapid (<60 min), low-cost, convenient, field-deployable sequence-specific nucleic acid-based amplification tests (NAATs) are described. A microfluidic point-of-care (POC) diagnostics test to quantify HIV viral load from blood samples serves as a representative and instructive example to discuss the technical issues and capabilities of “lab on a chip” NAAT devices. A portable, miniaturized POC NAAT with performance comparable to conventional PCR (polymerase-chain reaction)-based tests in clinical laboratories can be realized with a disposable, palm-sized, plastic microfluidic chip in which: (1) nucleic acids (NAs) are extracted from relatively large (~mL) volume sample lysates using an embedded porous silica glass fiber or cellulose binding phase (“membrane”) to capture sample NAs in a flow-through, filtration mode; (2) NAs captured on the membrane are isothermally (~65 °C) amplified; (3) amplicon production is monitored by real-time fluorescence detection, such as with a smartphone CCD camera serving as a low-cost detector; and (4) paraffin-encapsulated, lyophilized reagents for temperature-activated release are pre-stored in the chip. Limits of Detection (LOD) better than 10³ virons/sample can be achieved. A modified chip with conduits hosting a diffusion-mode amplification process provides a simple visual indicator to readily quantify sample NA template. In addition, a companion microfluidic device for extracting plasma from whole blood without a centrifuge, generating cell-free plasma for chip-based molecular diagnostics, is described. Extensions to a myriad of related applications including, for example, food testing, cancer screening, and insect genotyping are briefly surveyed.

A Strategy for Minimizing Background Signal in Autoinductive Signal Amplification Reactions for Point-of-Need Assays

Rapid point-of-need assays are used to detect abundant biomarkers. The development of in situ signal amplification reactions could extend these assays to screening and triaging of patients for trace levels of biomarkers, even in resource-limited settings. We, and others, have developed small molecule-based in situ signal amplification reactions that eventually may be useful in this context. Herein we describe a design strategy for minimizing background signal that may occur in the absence of the target analyte, thus moving this in situ signal amplification approach one step closer to practical applications. Specifically, we describe allylic ethers as privileged connectors for linking detection and propagating functionality in a small molecule signal amplification reagent. Allylic ethers minimize background reactions while still enabling controlled release of a propagating signal in order to continue the signal amplification reaction. This paper characterizes the ability of allylic ethers to provide an amplified response, and offers insight into additional design considerations that are needed before in situ small molecule-based signal amplification becomes a viable strategy for point-of-need diagnostics.

Compact multi-channel surface plasmon resonance sensor for real-time multi-analyte biosensing

A compact multi-channel surface plasmon resonance (SPR) biosensor is demonstrated based on a tablet as the measurement platform. The SPR biosensor employs a bundle of fiber-optic SPR sensors as the multiplexed sensing elements that are illuminated by a light-emitting diode (LED) plane light source and detected by a cordless camera. The multi-channel SPR biosensor was based on optical fiber components for precise, label-free and high-throughput detection without the use of complex, specialized or fragile instrumentation that would require optical calibration. The reference and control channels compensated for the fluctuation of the LED light source and the bulk refractive index, increasing the accuracy and reliability of the biosensor. The multi-channel SPR biosensor was applied for multi-analyte biosensing of immunoglobulin G (IgG) and concanavalin A (Con A). The channels functionalized with staphylococcal protein A (SPA) and ribonuclease B (RNase B) only showed relative intensity responses to their corresponding analytes. Moreover, the multi-channel SPR sensors responded to the specific detection of IgG and Con A with an approximately linear relative intensity response to the analyte concentration. Hence, multiple analytes were simultaneously and quantitatively detected with the multi-channel SPR biosensor. This compact, cost-effective multi-channel SPR biosensor is adapted for point-of-care tests, which are important in healthcare and environmental monitoring and for biomolecular interaction analysis.

A Rapid and Low-Cost PCR Thermal Cycler for Low Resource Settings

BACKGROUND

Many modern molecular diagnostic assays targeting nucleic acids are typically confined to developed countries or to the national reference laboratories of developing-world countries. The ability to make technologies for the rapid diagnosis of infectious diseases broadly available in a portable, low-cost format would mark a revolutionary step forward in global health. Many molecular assays are also developed based on polymerase chain reactions (PCR), which require thermal cyclers that are relatively heavy (>20 pounds) and need continuous electrical power. The temperature ramping speed of most economical thermal cyclers are relatively slow (2 to 3 °C/s) so a polymerase chain reaction can take 1 to 2 hours. Most of all, these thermal cyclers are still too expensive ($2k to $4k) for low-resource setting uses.

METHODOLOGY/PRINCIPAL FINDINGS

In this article, we demonstrate the development of a low-cost and rapid water bath based thermal cycler that does not require active temperature control or continuous power supply during PCR. This unit costs $130 to build using commercial off-the-shelf items. The use of two or three vacuum-insulated stainless-steel Thermos food jars containing heated water (for denaturation and annealing/extension steps) and a layer of oil on top of the water allow for significantly stabilized temperatures for PCR to take place. Using an Arduino-based microcontroller, we automate the "archaic" method of hand-transferring PCR tubes between water baths.

CONCLUSIONS/SIGNIFICANCE

We demonstrate that this innovative unit can deliver high speed PCR (17 s per PCR cycle) with the potential to go beyond the 1,522 bp long amplicons tested in this study and can amplify from templates down to at least 20 copies per reaction. The unit also accepts regular PCR tubes and glass capillary tubes. The PCR efficiency of our thermal cycler is not different from other commercial thermal cyclers. When combined with a rapid nucleic acid detection approach, the thermos thermal cycler (TTC) can enable on-site molecular diagnostics in low-resource settings.

Toward point-of-care diagnostics with consumer electronic devices: the expanding role of nanoparticles

A review of the role that nanoparticles can play in point-of-care diagnostics that utilize consumer electronic devices such as cell phones and smartphones for readout, including an overview of important concepts and examples from the literature.

Paper-based assay of antioxidant activity using analyte-mediated on-paper nucleation of gold nanoparticles as colorimetric probes

With the increasing interest in the health benefits arising from the consumption of dietary products rich in antioxidants, there exists a clear demand for easy-to-use and cost-effective tests that can be used for the identification of the antioxidant power of food products. Paper-based analytical devices constitute a remarkable platform for such expedient and low-cost assays with minimal external resources but efforts in this direction are still scarce. In this work we introduce a new paper-based device in the form of a sensor patch that enables the determination of antioxidant activity through analyte-driven on-paper formation of gold nanoparticles. The principle of detection capitalizes, for the first time, on the on-paper nucleation of gold ions to its respective nanoparticles, upon reduction by antioxidant compounds present in an aqueous sample. The ensuing chromatic transitions, induced on the paper surface, are used as an optical "signature" of the antioxidant strength of the solution. The response of the paper-based sensor was evaluated against a large variety of antioxidant species and the respective dose response curves were constructed. On the basis of these data, the contribution of each species according to its chemical structure was elucidated. For the analysis of real samples, a concentration-dependent colorimetric response was established against Gallic acid equivalents over a linear range of 10 μM-1.0 mM, with detection limits at the low and ultra-low μM levels (i.e. <1.0 μM) and satisfactory precision (RSD=3.6-12.6%). The sensor has been tested for the assessment of antioxidant activity in real samples (teas and wines) and the results correlated well with commonly used antioxidant detection methods. Importantly, the sensor performed favorably for long periods of time when stored at moisture-free and low temperature conditions without losing its activity thus posing as an attractive alternative to the assessment of antioxidant activity without specialized equipment. The use of the sensor by non-experts for a rapid assessment of natural products in field testing is envisioned. Importantly, we demonstrate for the first time that analyte-mediated growth of nanomaterials directly on the paper surface could open new opportunities in paper-based analytical devices.