Comparison of SYTO9 and SYBR Green I for real-time polymerase chain reaction and investigation of the effect of dye concentration on amplification and DNA melting curve analysis

Biodegradation of phenol-contaminated soil and plant growth promotion by Myroides xuanwuensis H13

Physicochemical methods for remediating phenol-contaminated soils are costly and inefficient, making biodegradation an environmentally friendly alternative approach. This study aims to screen for potential phenol-degrading bacteria and to verify the removal capacities of a selected strain in a bioaugmentation experiment at the greenhouse level using Brassica chinensis L. (Chinese cabbage) as the model plant and phenol-contaminated soil. In parallel, pot experiments were conducted using a collaborative approach based on this model system. We found that Myroides xuanwuensis strain H13 showed a high degradation capability, with a 97.67% efficiency in degrading 100 mg/L phenol. Under shaking flask conditions, H13 facilitated the solubilization of tricalcium phosphate and potassium feldspar powder. Pot experiments suggested a phenol removal percentage of 89.22% and enhanced availability of soil phosphorus and potassium for plants with H13 inoculation. In this case, the abundance of soil microbes and the activity of soil enzymes significantly increased as well. Furthermore, both photosynthesis and the antioxidant system in Chinese cabbage were enhanced following H13 inoculation, resulting in its increased yield and quality. Partial least squares path modeling revealed that H13 can primarily affect plant root growth, with a secondary impact on photosynthesis. These findings highlight the potential of biodegradation from phenol-degrading bacteria as a promising strategy for efficient phenol removal from soil while promoting plant growth and health.IMPORTANCEThis study is significant for environmental remediation and agriculture by its exploration of a more environmentally friendly and cost-effective bio-strategy in treating phenol-contaminated soil. These findings have essential implications for environmental remediation efforts and sustainable agriculture. By utilizing the biodegradation capabilities of Myroides xuanwuensis strain H13, it is possible to remove phenol contaminants from the soil efficiently, reducing their negative effects. Furthermore, the enhanced growth and health of the Chinese cabbage plants indicate the potential of this approach to promote sustainable crop production.

Techniques, procedures, and applications in host genetic analysis

This chapter overviews genetic techniques' fundamentals and methodological features, including different approaches, analyses, and applications that have contributed to advancing health and disease. The aim is to describe laboratory methodologies and analyses employed to understand the genetic landscape of different biological contexts, from conventional techniques to cutting-edge technologies. Besides describing detailed aspects of the polymerase chain reaction (PCR) and derived types as one of the principles for many novel techniques, we also discuss microarray analysis, next-generation sequencing, and genome editing technologies such as transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems. These techniques study several phenotypes, ranging from autoimmune disorders to viral diseases. The significance of integrating diverse genetic methodologies and tools to understand host genetics comprehensively and addressing the ethical, legal, and social implications (ELSI) associated with using genetic information is highlighted. Overall, the methods, procedures, and applications in host genetic analysis provided in this chapter furnish researchers and practitioners with a roadmap for navigating the dynamic landscape of host-genome interactions.

Structural basis for dimerization of a paramyxovirus polymerase complex

The transcription and replication processes of non-segmented, negative-strand RNA viruses (nsNSVs) are catalyzed by a multi-functional polymerase complex composed of the large protein (L) and a cofactor protein, such as phosphoprotein (P). Previous studies have shown that the nsNSV polymerase can adopt a dimeric form, however, the structure of the dimer and its function are poorly understood. Here we determine a 2.7 Å cryo-EM structure of human parainfluenza virus type 3 (hPIV3) L-P complex with the connector domain (CD') of a second L built, while reconstruction of the rest of the second L-P obtains a low-resolution map of the ring-like L core region. This study reveals detailed atomic features of nsNSV polymerase active site and distinct conformation of hPIV3 L with a unique β-strand latch. Furthermore, we report the structural basis of L-L dimerization, with CD' located at the putative template entry of the adjoining L. Disruption of the L-L interface causes a defect in RNA replication that can be overcome by complementation, demonstrating that L dimerization is necessary for hPIV3 genome replication. These findings provide further insight into how nsNSV polymerases perform their functions, and suggest a new avenue for rational drug design.

A Fusion of Taq DNA Polymerase with the CL7 Protein from Escherichia coli Remarkably Improves DNA Amplification

DNA polymerases are important enzymes that synthesize DNA molecules and therefore are critical to various scientific fields as essential components of in vitro DNA synthesis reactions, including PCR. Modern diagnostics, molecular biology, and genetic engineering require DNA polymerases with improved performance. This study aimed to obtain and characterize a new CL7-Taq fusion DNA polymerase, in which the DNA coding sequence of Taq DNA polymerase was fused with that of CL7, a variant of CE7 (Colicin E7 DNase) from Escherichia coli. The resulting novel recombinant open reading frame was cloned and expressed in E. coli. The recombinant CL7-Taq protein exhibited excellent thermostability, extension rate, sensitivity, and resistance to PCR inhibitors. Our results showed that the sensitivity of CL7-Taq DNA polymerase was 100-fold higher than that of wild-type Taq, which required a template concentration of at least 1.8 × 105 nM. Moreover, the extension rate of CL7-Taq was 4 kb/min, which remarkably exceeded the rate of Taq DNA polymerase (2 kb/min). Furthermore, the CL7 fusion protein showed increased resistance to inhibitors of DNA amplification, including lactoferrin, heparin, and blood. Single-cope human genomic targets were readily available from whole blood, and pretreatment to purify the template DNA was not required. Thus, this is a novel enzyme that improved the properties of Taq DNA polymerase, and thus may have wide application in molecular biology and diagnostics.

Mayaro virus detection by integrating sample preparation with isothermal amplification in portable devices

Mayaro virus (MAYV) is an emerging mosquito-borne alphavirus that causes clinical symptoms similar to those caused by Chikungunya virus (CHIKV), Dengue virus (DENV), and Zika virus (ZIKV). To differentiate MAYV from these viruses diagnostically, we have developed a portable device that integrates sample preparation with real-time, reverse-transcription, loop-mediated isothermal amplification (rRT-LAMP). First, we designed a rRT-LAMP assay targeting MAYV's non-structural protein (NS1) gene and determined the limit of detection of at least 10 viral genome equivalents per reaction. The assay was specific for MAYV, without cross-reactions with CHIKV, DENV, or ZIKV. The rRT-LAMP assay was integrated with a sample preparation device (SPD) wherein virus lysis and RNA enrichment/purification were carried out on the spot, without requiring pipetting, while subsequent real-time amplification device (RAD) enables virus detection at the point of care (POC). The functions of our platform were demonstrated using purified MAYV RNA or blood samples containing viable viruses. We have used the devices for detection of MAYV in as short as 13 min, with limit of detection to as low as 10 GEs/reaction.

Construction and optimization of a multiplex PMAxx-qPCR assay for viable Bacillus cereus and development of a detection kit

In this study, a PMAxx-qPCR method for the detection and quantification of viable Bacillus cereus (B. cereus) was established based on the cesA gene that is involved in cereulide synthesis, enterotoxin gene bceT and hemolytic enterotoxin gene hblD combined with modified propidium monoazide (PMAxx). The sensitivity detection limit of the method was as follows: the DNA extracted by the kit reached 140 fg/μL, and the bacterial suspension without enrichment reached 2.24 × 10¹ CFU/mL; 14 nonB. cereus strains of the 17 tested strains all tested as negative, whereas the 2 strains of B. cereus carrying the target virulence gene(s) could be accurately detected. In terms of application, we assembled the constructed PMAxx-qPCR reaction into a detection kit and evaluated its application performance. The results showed that the detection kit has high sensitivity, strong anti-interference capability, and has good application potential. The purpose of this study is to provide a reliable detection method for the prevention and traceability of B. cereus infections.

Real-Time PCR High-Resolution Melting Assays for the Detection of Foodborne Pathogens

Real-time PCR high-resolution melting assays are a method for the identification of single nucleotide polymorphisms (SNPs). The assay is performed by amplifying a short DNA fragment using a specific primer pair flanking a target SNP in the presence of a high-resolution melting dye. The HRM analysis of amplicons groups the samples based on the differences in the melting temperature and the shape of the melt curves, facilitating a convenient genotyping of samples. This chapter describes the steps and considerations of real-time PCR HRM assay standardization.

Two Leishmania species separation targeting the ITS-rDNA and Cyt b genes by developing and evaluating HRM- qPCR

BACKGROUND

Incidence of Cutaneous Leishmaniasis as an infectious and neglected disease is increasing, for the diagnosis of which several traditional methods and conventional PCR techniques have been developed, employing different genes for species identification.

METHODS

Leishmania parasites were sampled, DNA was extracted, and new specific and sensitive primers were designed. Two ITS-rDNA and Cyt b genes were targeted by qPCR using the High- Resolution Melting method to identify Leishmania parasites. The standard curves were drawn, compared, and identified by high-resolution melting curve analysis.

RESULTS

Melting temperature and Cycle of Threshold of ITS-rDNA was higher than Cyt b but Cyt b was more sensitive than ITS-rDNA when Leishmania major and Leishmania tropica were analyzed and evaluated. By aligning melt curves, normalizing fluorescence curves, and difference plotting melt curves, each Leishmania species was distinguished easily. L. major and L. tropica were separated at 83.6 °C and 84.7 °C, respectively, with less than 0.9 °C of temperature difference. Developing sensitivity and specificity of real-time PCR based on EvaGreen could detect DNA concentration to less than one pmol.

CONCLUSIONS

Precise identification of Leishmania parasites is crucial for strategies of disease control. Real-time PCR using EvaGreen provides rapid, highly sensitive, and specific detection of parasite's DNA. The modified High-Resolution Melting could determine unique curves and was able to detect single nucleotide polymorphisms according to small differences in the nucleotide content of Leishmania parasites.

Screening of phosphate-solubilizing bacteria and their abilities of phosphorus solubilization and wheat growth promotion

BACKGROUND

Phosphate-solubilizing bacteria (PSB) can enhance plant growth and phosphorus (P) solubilization, it also has been reported to reduce the negative effects of overused agricultural fertilizer in farmland and protect the soil environment. However, the mechanism behind this interaction has not been fully elucidated.

RESULTS

In this study, we screened out Pseudomonas moraviensis, Bacillus safensis, and Falsibacillus pallidus which can both solubilize P efficiently and produce indole-3-acetic acid (IAA) from sandy fluvo-aquic soils. The yield of wheat (Triticum aestivum) under PSB inoculation significantly increased up to 14.42% (P < 0.05) compared with the control treatment in phosphate fertilizer-used farmland. Besides promoting wheat growth, we found the labile P fraction in soil was significantly increased by over 122.04% (P < 0.05) under PSB inoculation compared with it in soils without, in parallel, the stable P fraction was significantly reduced by over 46.89% (P < 0.05). Furthermore, PSB inoculation increased the soil microbial biomass and activity, indicating that PSB screened out in this work performed a remarkable ability to colonize the soils in the wheat field.

CONCLUSION

PSB from sandy fluvo-aquic soil improve wheat growth and crop productivity by increasing the labile P fraction and IAA content in the greenhouse and wheat field. Our work provides an environment and economy-friendly bacterial resource that potentially promotes sustainable agricultural development in the long term.

Visual LAMP method for the detection of Vibrio vulnificus in aquatic products and environmental water

Background

A visual, rapid, simple method was developed based on a loop-mediated isothermal amplification (LAMP) assay to detect Vibrio vulnificus in aquatic products and aquaculture waters.

Results

Genomic DNA was extracted from Vibrio vulnificus using the boiling method, and optimized primers were used to detect the gyrB gene using a visual LAMP method. The sensitivity of the assay was 10 fg/μL, and the obtained results were stable and reliable. Out of 655 aquatic product samples and 558 aquaculture water samples, the positive rates of Vibrio vulnificus detection were 9.01% and 8.60%, respectively, which are markedly higher than those of the traditional culture identification methods.

Conclusion

The relatively simple technical requirements, low equipment cost, and rapid detection make the visual LAMP method for the detection of Vibrio vulnificus a convenient choice for field detection in the aquaculture industry.

Optimized Protocol for Microalgae DNA Staining with SYTO9/SYBR Green I, Based on Flow Cytometry and RSM Methodology: Experimental Design, Impacts and Validation

Multiple fluorochromes are extensively used to investigate different microalgal aspects, such as viability and physiology. Some of them can be used to stain nucleic acids (DNA). Well-known examples are SYBR Green I and SYTO 9, the latter of which offers several advantages, especially when combined with flow cytometry (FCM)—a powerful method for studying microalgal population heterogeneity and analyzing their cell cycles. However, the effects of these dyes on the microalgae cell physiology have not been fully elucidated yet. A statistical experimental design, using response surface methodology (RSM) with FCM was applied in this study to optimize the DNA staining of a non-conventional microalgae, Chromochloris zofingiensis, with SYBR Green I and SYTO 9, and to optimize the variables affecting staining efficiency, i.e., the dye concentration, incubation time and staining temperature. We found that none of these factors affects the staining efficiency, which was not less than 99.65%. However, for both dyes, the dye concentration was shown to be the most significant factor causing cell damage (p-values: 0.0003; <0.0001) for SYBR Green I and SYTO 9, respectively. The staining temperature was only significant for SYTO 9 (p-value: 0.0082), and no significant effect was observed regarding the incubation time for both dyes. The values of the optimized parameters (0.5 µM, 05 min and 25 °C) for SYTO 9 and (0.5 X, 5 min and 25 °C) for SYBR Green I resulted in the maximum staining efficiency (99.8%; 99.6%), and the minimum damaging effects (12.86%; 13.75%) for SYTO 9 and SYBR Green I, respectively. These results offer new perspectives for improving the use of DNA staining fluorochromes and provides insights into their possible side effects on microalgae.

Multiplex Quantitative Real-Time Polymerase Chain Reaction and High-Resolution Melting Analysis for Identification of a Couple At-Risk of Having a Newborn with Severe Thalassemia

Many polymerase chain reaction (PCR)-based techniques have been used for routine diagnosis of α- and β-thalassemias. However, most require a multi step of post-PCR processes that are time-consuming and labor-intensive procedures. This study reported the successful use of multiplex quantitative real-time PCR (qPCR), with high-resolution melting (HRM) analysis for diagnosis of two common deletional α⁰-thalassemia (α⁰-thal) and 15 common β-thalassemia (β-thal) mutations, in order to identify a couple at-risk of having a newborn with severe thalassemia in the northern region of Thailand. With this approach, 22 (7.2%) of 306 couples were diagnosed as being at-risk for having a child with severe thalassemia, including three homozygous α⁰-thal, five homozygous β-thal and 14 Hb E (HBB: c.79G>A)/β⁰-thal disease. Our findings indicated that multiplex qPCR with HRM is applicable for routine molecular diagnosis in order to identify a couple at-risk of having a newborn with severe thalassemia, especially in an endemic region.

The Potential Use of Isothermal Amplification Assays for In-Field Diagnostics of Plant Pathogens

Rapid, sensitive, and timely diagnostics are essential for protecting plants from pathogens. Commonly, PCR techniques are used in laboratories for highly sensitive detection of DNA/RNA from viral, viroid, bacterial, and fungal pathogens of plants. However, using PCR-based methods for in-field diagnostics is a challenge and sometimes nearly impossible. With the advent of isothermal amplification methods, which provide amplification of nucleic acids at a certain temperature and do not require thermocyclic equipment, going beyond the laboratory has become a reality for molecular diagnostics. The amplification stage ceases to be limited by time and instruments. Challenges to solve involve finding suitable approaches for rapid and user-friendly plant preparation and detection of amplicons after amplification. Here, we summarize approaches for in-field diagnostics of phytopathogens based on different types of isothermal amplification and discuss their advantages and disadvantages. In this review, we consider a combination of isothermal amplification methods with extraction and detection methods compatible with in-field phytodiagnostics. Molecular diagnostics in out-of-lab conditions are of particular importance for protecting against viral, bacterial, and fungal phytopathogens in order to quickly prevent and control the spread of disease. We believe that the development of rapid, sensitive, and equipment-free nucleic acid detection methods is the future of phytodiagnostics, and its benefits are already visible.

Evaluation of High Resolution Melting (HRM) Analysis for Meat Species Identification of Raw and Cooked Meat

The current study aimed to examine a real-time PCR assay with high-resolution melting (HRM) analysis for the species identification of minced meat samples. Meat samples from several animal species were purchased and minced separately or as a mixture of two species. DNA was extracted from all meat samples and subjected to real-time PCR assay by amplifying species-specific mitochondrial cytochrome b regions. Regarding the meat mixtures, two separate melting curves with specific melt peak temperatures (Tm) were detected. Additionally, DNA from each species was quantified, based on the calibration curves. The results showed that a real-time PCR assay with HRM analysis is suitable for the species identification of meat products, and could be used for the detection of meat frauds.

Clinical and etiological analysis of co-infections and secondary infections in COVID-19 patients: An observational study

Background

Co‐infections, secondary bacterial or fungal infections, are important risk factors for poor outcomes in viral infections. The prevalence of co‐infection and secondary infection in patients infected with SARS‐CoV‐2 is not well understood.

Aims

To investigate the role of co‐infections and secondary infections in disease severity of hospitalized individuals with COVID‐19.

Materials and Methods

A retrospective study was carried out between 11 January 2020 and 1 March 2020 among 408 laboratory confirmed COVID‐19 patients in China. These patients were divided into three groups based on disease severity: mild or moderate, severe, or critically ill. Microbiological pathogens in blood, urine, and respiratory tract specimens were detected by the combination of culture, serology, polymerase chain reaction, and metagenomic next‐generation sequencing (mNGS).

Results

The median age of participants was 48 years (IQR 34–60 years). Fifty‐two patients (12.7%) had at least one additional pathogen, 8.1% were co‐infected, and 5.1% had a secondary infection. There were 13 Mycoplasma pneumoniae cases, 8 Haemophilus influenzae cases, 8 respiratory viruses, and 3 Streptococcus pneumoniae cases, primarily detected in mild and moderate COVID‐19 patients. Hospital‐acquired infection pathogens were more common in critically ill patients. Compared to those without additional pathogens, patients with co‐infections and/or secondary infections were more likely to receive antibiotics (p < 0.001) and have elevated levels of d‐dimer (p = 0.0012), interleukin‐6 (p = 0.0027), and procalcitonin (p = 0.0002). The performance of conventional culture was comparable with that of mNGS in diagnosis of secondary infections.

Conclusion

Co‐infections and secondary infections existed in hospitalized COVID‐19 patients and were relevant to the disease severity. Screening of common respiratory pathogens and hospital infection control should be strengthened.

Tillage, Mulching and Nitrogen Fertilization Differentially Affects Soil Microbial Biomass, Microbial Populations and Bacterial Diversity in a Maize Cropping System

Determination of biologically active components of the soil organic matter, such as soil microbial biomass carbon (C) and nitrogen (N) can be used as indicators for variations in soil productivity due to changes in soil management. Soil agronomic management practices bring about changes in the physical and chemical properties of the soil, resulting in variations in soil microbial biomass and microbial diversity. The effects of tillage, mulch and inorganic fertilizers on soil microbial biomass C and N, microbial populations and bacterial diversity were determined from the treatment combinations which had been applied for 5 years in Central Kenyan Highlands. The test crop used was maize (Zea mays L.). The study involved conventional and minimum tillage systems, mulching and inorganic fertilizers (120 kg N/ha). Tillage (P &lt; 0.001), mulch (P &lt; 0.001), and fertilizer (P = 0.009) significantly affected soil microbial biomass C and N whereby minimum tillage and mulch increased soil microbial biomass C and N. Interestingly, minimum tillage and mulch recorded the highest bacteria and fungi CFUs compared to conventional tillage and inorganic fertilizers. Only fertilizer and mulch (P &lt; 0.001) had significant effect on actinobacteria CFUs. Amplified ribosomal DNA analysis (ARDRA) showed that the highest genetic distance of 0.611 was recorded between treatments conventional tillage + no mulch + no NPK fertilizer and conventional tillage + no mulch + NPK fertilizer. The results demonstrate that minimum tillage and mulching are attractive soil agronomic management practices since they increase soil microbial biomass and bacterial diversity in agricultural soils.

Development of High Resolution Melting Analysis as a Diagnostic Tool for Molecular Detection of Toxoplasma Infection in Pregnant Women and HIV Positive Cases

Background

Toxoplasma gondii is an obligate intracellular protozoan with worldwide distribution. Diagnosis of toxoplasmosis is a very critical issue, especially in pregnant women and immunocompromised patients. The aim of this study was rapid detection of T. gondii DNA in peripheral blood samples (PBS) employing HRM technique and using RE gene.

Methods

Totally, 242 samples from pregnant women and human immunodeficiency virus (HIV) patients were collected from different hospitals and medical centers of Tehran during Oct 2017 to Dec 2018. High resolution melting analysis (HRM) using partial sequences of repetitive element (RE) gene was done and compared with ELISA test.

Results

Overall, 51 were positive for acute toxoplasmosis that among them, 12 and 20 reported as positive in pregnant women and HIV⁺ patients, respectively using HRM technique. Among 70 patients in chronic phase of disease, 10 and 3 samples were reported as positive for pregnant women and HIV⁺ patients respectively. From 121 negative control, 3 (4.62%) samples associated with HIV⁺ patients, showed positive real-time PCR and HRM analysis results.

Conclusion

For the first time, HRM technique via employing RE gene was used for detection of T. gondii infection in PBS. This method is suitable, helpful and in parallel with serological methods for early diagnosis of acute as well as active form of toxoplasmosis in pregnant women and HIV⁺ patients. The use of techniques based on melt curve and through employing next-generation dyes for diagnosis of T. gondii would be accessible for patients in developing countries.

Development and evaluation of 4 loop-mediated isothermal amplification assays to detect mastitis-causing bacteria in bovine milk samples

Farmers prefer fast, sensitive, and on-site tests for treatment decisions on mastitis. Due to the time to results of the currently available diagnostic tools, these are rarely used for that purpose. Genotypic tests that do not require a growth step may be suitable for on-site testing, for example loop-mediated isothermal amplification (LAMP), which has been described as a sensitive test that can be used on-site. Therefore, this study aimed to develop and evaluate LAMP assays for the detection of a subset of mastitis-causing pathogens, Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus spp., in milk from cows with clinical mastitis. Furthermore, a generic nucleic acid lateral flow immunoassay (NALFIA) was evaluated as a potential on-site readout of the LAMP assays. For each assay of LAMP and NALFIA, the limit of detection and analytical specificity were determined using isolates, and the diagnostic specificity was determined using selected samples with known etiology. In addition, the diagnostic specificity of LAMP was determined using field samples with unknown etiology at testing. Bacteriological culture with identification by mass spectrometry was used as a reference method. The 4 assays had a kappa ≥0.73 with the reference method when testing the selected samples, but ≥0.47 when testing field samples. After correcting for prevalence, kappa was ≥0.80 for the E. coli, K. pneumoniae, and Staph. aureus assays. The Streptococcus spp. assay had a kappa of 0.47 (0.48 after correction) with the reference method, probably caused by the assay broadly targeting a genus instead of a particular species. The NALFIA readout was found to have kappa ≥0.81 for the E. coli, Staph. aureus, and Streptococcus spp. assays at a generic runtime, but for the K. pneumoniae assay a shorter runtime could be used. In conclusion, LAMP is a promising method for fast on-site tests for mastitis-causing pathogens if the current elaborate method for sample preparation is replaced by a simplified protocol. The NALFIA is an easy and reliable readout for on-site use, with the observation that for the current assay designs a generic runtime is not yet possible for the chosen set of pathogens. If associated with a simple and fast sample preparation protocol, the combination of LAMP and NALFIA has the potential to enable fast and reliable on-site testing of clinical mastitis milk samples.

Loop Mediated Isothermal Amplification: Principles and Applications in Plant Virology

In the last decades, the evolution of molecular diagnosis methods has generated different advanced tools, like loop-mediated isothermal amplification (LAMP). Currently, it is a well-established technique, applied in different fields, such as the medicine, agriculture, and food industries, owing to its simplicity, specificity, rapidity, and low-cost efforts. LAMP is a nucleic acid amplification under isothermal conditions, which is highly compatible with point-of-care (POC) analysis and has the potential to improve the diagnosis in plant protection. The great advantages of LAMP have led to several upgrades in order to implement the technique. In this review, the authors provide an overview reporting in detail the different LAMP steps, focusing on designing and main characteristics of the primer set, different methods of result visualization, evolution and different application fields, reporting in detail LAMP application in plant virology, and the main advantages of the use of this technique.

PCR inhibition in qPCR, dPCR and MPS-mechanisms and solutions

DNA analysis has seen an incredible development in terms of instrumentation, assays and applications over the last years. Massively parallel sequencing (MPS) and digital PCR are now broadly applied in research and diagnostics, and quantitative PCR is used for more and more practises. All these techniques are based on in vitro DNA polymerization and fluorescence measurements. A major limitation for successful analysis is the various sample-related substances that interfere with the analysis, i.e. PCR inhibitors. PCR inhibition affects library preparation in MPS analysis and skews quantification in qPCR, and some inhibitors have been found to quench the fluorescence of the applied fluorophores. Here, we provide a deeper understanding of mechanisms of specific PCR inhibitors and how these impact specific analytical techniques. This background knowledge is necessary in order to take full advantage of modern DNA analysis techniques, specifically for analysis of samples with low amounts of template and high amounts of background material. The classical solution to handle PCR inhibition is to purify or dilute DNA extracts, which leads to DNA loss. Applying inhibitor-tolerant DNA polymerases, either single enzymes or blends, provides a more straightforward and powerful solution. This review includes mechanisms of specific PCR inhibitors as well as solutions to the inhibition problem in relation to cutting-edge DNA analysis.

Fractal LAMP: Label-Free Analysis of Fractal Precipitate for Digital Loop-Mediated Isothermal Nucleic Acid Amplification

Nucleic acid amplification assays including loop-mediated isothermal amplification (LAMP) are routinely used in diagnosing diseases and monitoring water and food quality. The results of amplification in these assays are commonly measured with an analog fluorescence readout, which requires specialized optical equipment and can lack quantitative precision. Digital analysis of amplification in small fluid compartments based on exceeding a threshold fluorescence level can enhance the quantitative precision of nucleic acid assays (i.e., digital nucleic acid amplification assays), but still requires specialized optical systems for fluorescence readout and the inclusion of a fluorescent dye. Here, we report Fractal LAMP, an automated method to detect amplified DNA in subnanoliter scale droplets following LAMP in a label-free manner. Our computer vision algorithm achieves high accuracy detecting DNA amplification in droplets by identifying LAMP byproducts that form fractal structures observable in brightfield microscopy. The capabilities of Fractal LAMP are further realized by developing a Bayesian model to estimate DNA concentrations for unknown samples and a bootstrapping method to estimate the number of droplets required to achieve target limits of detection. This digital, label-free assay has the potential to lower reagent and reader cost for nucleic acid measurement while maintaining high quantitative accuracy over 3 orders of magnitude of concentration.

Detection of extended-spectrum beta-lactamase cefotaxime resistance and virulence genes in Escherichia coli by duplex quantitative real-time PCR and melt curve analysis

Emerging virulent and antibiotic-resistant pathogens present a global public health risk. Routine monitoring of prevalence within the clinical, environmental and food production setting is vital. Quantitative real-time PCR (qPCR) coupled with melting curve analysis can rapidly and accurately characterize pathogens. We evaluated commercial qPCR mixes based on SYBR Green l and EvaGreen for developing an assay for simultaneously detecting antibiotic resistance (extended-spectrum beta-lactamase, ESBL and bla_CTX-M ) and virulence (stx1, stx2 and eae) genes in Escherichia coli (n = 12) isolated from irrigation water and irrigated vegetables. SYBR Green and EvaGreen detected two amplicons (stx1 and bla_CTX-M ) and (stx2 and eae) in a single reaction. A higher mean melting temperature (T_m ) separation between targeted amplicons and smoother melting curves were observed with the EvaGreen suggesting better performance when targeting multiple amplicons. Through simple stepwise optimization of DNA, cycling, primers, reaction volume and melting curve scanning rate, we adopted a conventional PCR assay for detection of large amplicons (375-1580 bp) for qPCR. This may facilitate development of cost-effective tailor-made assays for rapid and accurate monitoring of emerging foodborne and environmental pathogens in resource constrained regions.

GLADS: A gel-less approach for detection of STMS markers in wheat and rice

Sequence tagged microsatellite site (STMS) are useful PCR based DNA markers. Wide genome coverage, high polymorphic index and co-dominant nature make STMS a preferred choice for marker assisted selection (MAS), genetic diversity analysis, linkage mapping, seed genetic purity analysis etc. Routine STMS analysis involving low-throughput, laborious and time-consuming polyacrylamide/agarose gels often limit their full utility in crop breeding experiments that involve large populations. Therefore, convenient, gel-less marker detection methods are highly desirable for STMS markers. The present study demonstrated the utility of SYBR Green dye based melt-profiling as a simple and convenient gel-less approach for detection of STMS markers (referred to as GLADS) in bread wheat and rice. The method involves use of SYBR Green dye during PCR amplification (or post-PCR) of STMS markers followed by generation of a melt-profile using controlled temperature ramp rate. The STMS amplicons yielded characteristic melt-profiles with differences in melting temperature (Tm) and profile shape. These characteristic features enabled melt-profile based detection and differentiation of STMS markers/alleles in a gel-less manner. The melt-profile approach allowed assessment of the specificity of the PCR assay unlike the end-point signal detection assays. The method also allowed multiplexing of two STMS markers with non-overlapping melt-profiles. In principle, the approach can be effectively used in any crop for STMS marker analysis. This SYBR Green melt-profiling based GLADS approach offers a convenient, low-cost (20-51%) and time-saving alternative for STMS marker detection that can reduce dependence on gel-based detection, and exposure to toxic chemicals.

Determination of live and dead Komagataeibacter xylinus cells and first attempt at precise control of inoculation in nanocellulose production

The timely enumeration of cells of nanocellulose-producing bacteria is challenging due to their unique growth properties. To better understand the metabolism of the bacteria and better control the concentration of living cells during cultivation, a prompt cell counting technology is crucial and urgently required. In this work, two fluorescent dyes, the asymmetrical anthocyanidin dye SYBR Green I (SG) and propidium iodide (PI), were first combined for Komagataeibacter xylinus species to determine live/dead bacterial cells quantitatively and promptly. The number of live and dead K. xylinus cells determined using an epifluorescence microscope corresponded well to the results obtained using a fluorescence microplate reader. The R² values were 0.9986 and 0.9920, respectively, and were similar to those obtained with the LIVE/DEAD^® BacLight^TM commercial kit. SG/PI double-staining showed proper efficiency in distinguishing live/dead cells for the K. xylinus strain (R²  = 0.9898). The technology was applied to standardize four different K. xylinus strains, and the initial cell concentration of the strains was precisely controlled (no significant difference among the strains, P> 0.05). The cellulose yield per live cell was calculated, and significant differences (P < 0.05) were found among the four strains in the following order: DHU-ATCC-1> DHU-ZCY-1> DHU-ZGD-1> ATCC 23770. The study shows (i) the application of the SG/PI staining to standardizing inocula for bacterial cellulose production so that a more accurate comparison can be made between different strains, and (ii) the lower cost of using SG rather than the SYTO 9 of the commercially available LIVE/DEAD^® BacLight^TM kit.

Classification of Multiple DNA Dyes Based on Inhibition Effects on Real-Time Loop-Mediated Isothermal Amplification (LAMP): Prospect for Point of Care Setting

LAMP has received great interest and is widely utilized in life sciences for nucleic acid analysis. To monitor a real-time LAMP assay, a fluorescence DNA dye is an indispensable component and therefore the selection of a suitable dye for real-time LAMP is a need. To aid this selection, we investigated the inhibition effects of twenty-three DNA dyes on real-time LAMP. Threshold time (T_t) values of each real-time LAMP were determined and used as an indicator of the inhibition effect. Based on the inhibition effects, the dyes were classified into four groups: (1) non-inhibition effect, (2) medium inhibition effect, (3) high inhibition effect, and (4) very high inhibition effect. The signal to noise ratio (SNR) and the limit of detection (LOD) of the dyes in groups 1, 2, and 3 were further investigated, and possible inhibition mechanisms of the DNA dyes on the real-time LAMP are suggested and discussed. Furthermore, a comparison of SYTO 9 in different LAMP reactions and different systems is presented. Of the 23 dyes tested, SYTO 9, SYTO 82, SYTO 16, SYTO 13, and Miami Yellow were the best dyes with no inhibitory effect, low LOD and high SNR in the real-time LAMP reactions. The present classification of the dyes will simplify the selection of fluorescence dye for real-time LAMP assays in point of care setting.

Effects of historic and projected climate change on the range and impacts of an emerging wildlife disease

The global trend of increasing environmental temperatures is often predicted to result in more severe disease epidemics. However, unambiguous evidence that temperature is a driver of epidemics is largely lacking, because it is demanding to demonstrate its role among the complex interactions between hosts, pathogens, and their shared environment. Here, we apply a three-pronged approach to understand the effects of temperature on ranavirus epidemics in UK common frogs, combining in vitro, in vivo, and field studies. Each approach suggests that higher temperatures drive increasing severity of epidemics. In wild populations, ranavirosis incidents were more frequent and more severe at higher temperatures, and their frequency increased through a period of historic warming in the 1990s. Laboratory experiments using cell culture and whole animal models showed that higher temperature increased ranavirus propagation, disease incidence, and mortality rate. These results, combined with climate projections, predict severe ranavirosis outbreaks will occur over wider areas and an extended season, possibly affecting larval recruitment. Since ranaviruses affect a variety of ectothermic hosts (amphibians, reptiles, and fish), wider ecological damage could occur. Our three complementary lines of evidence present a clear case for direct environmental modulation of these epidemics and suggest management options to protect species from disease.

Data for homogeneous thermofluorimetric assays for ethanolamine using aptamers and a PCR instrument

The data presented in this article describe the quantitative detection of small molecules e.g. ethanolamine through the shifts in the melting temperatures of aptamer beacons presented in the research article entitled “An aptamer based thermofluorimetric assay for ethanolamine” [1]. The data include prediction and optimization of the folding structure of the aptamers. Moreover, the data from using intercalating dyes such as SYBR green is included for comparison. The presented data could be used for the design of other small molecules sensing platforms using aptamers.

Phylogenetic mapping of scale nanostructure diversity in snakes

BACKGROUND

Many species of snakes exhibit epidermal surface nanostructures that form complex motifs conferring self-cleaning properties, and sometimes structural iridescence, to their skin.

RESULTS

Using confocal microscopy, we show that these specialised cells can be greatly elongated along their left-right axis and that different types of nanostructures are generated by cell borders and cell surface. To characterise the complexity and diversity of these surface gratings, we analysed scanning electron microscopy images of skin sheds from 353 species spanning 19 of the 26 families of snakes and characterised the observed nanostructures with four characters. The full character matrix, as well as one representative SEM image of each of the corresponding species, is available as a MySQL relational database at https://snake-nanogratings.lanevol.org . We then performed continuous-time Markov phylogenetic mapping on the snake phylogeny, providing an evolutionary dynamical estimate for the different types of nanostructures. These analyses suggest that the presence of cell border digitations is the ancestral state for snake skin nanostructures which was subsequently and independently lost in multiple lineages. Our analyses also indicate that cell shape and cell border shape are co-dependent characters whereas we did not find correlation between a simple life habit classification and any specific nanomorphological character.

CONCLUSIONS

These results, compatible with the fact that multiple types of nanostructures can generate hydrophobicity, suggest that the diversity and complexity of snake skin surface nano-morphology are dominated by phylogenetic rather than habitat-specific functional constraints. The present descriptive study opens the perspective of investigating the cellular self-organisational cytoskeletal processes controlling the patterning of different skin surface nanostructures in snakes and lizards.

Development and application of a qPCR assay targeting Ichthyophthirius multifiliis in environmental water samples

Ichthyophthirius multifiliis (Ich) is a globally distributed, freshwater parasitic ciliate that infects wild and cultured fishes. It has a direct, temperature-dependent life cycle that enables rapid multiplication when hosts are plentiful and environmental conditions are favorable. Accurate detection is central to the control of Ich infections and prevention of host mortality, particularly in wild systems where chemical treatments are not feasible. In the Klamath River, California, USA, the parasite threatens pre-spawning adult salmon Oncorhynchus spp. Currently, Ich is monitored by lethal sampling of fish hosts and visual quantification of parasite load. This method is insensitive to light infections, contributes to pre-spawn mortality of wild salmon, and does not allow for population-level disease risk assessments. We developed and applied an alternate sampling method based on molecular analysis of water samples for parasite DNA. We sequenced the small subunit ribosomal DNA (ssrDNA) of Ich isolates collected from the Klamath River, and then developed and validated a novel qPCR assay (SYTO9) that targets Ich ssrDNA. Our assay has better specificity than previously published assays, with strong linearity, efficiency and repeatability. The limit of detection was 50 copies of ssrDNA, equivalent to ~2 theronts in a sample. We found that Ich abundance in environmental water samples collected from the lower Klamath River from July to October, 2014 through 2016, related to observed parasite load on salmon sampled concurrently, indicating that the qPCR assay could be a useful monitoring tool for Ich in the Klamath River, with applications beyond the region.

Quantification of Malassezia pachydermatis by real-time PCR in swabs from the external ear canal of dogs

Malassezia pachydermatis is part of the normal microbiota of canine skin and external ear canal, and is also associated with otitis externa in dogs. Laboratory detection of Malassezia otitis relies on the presence of elevated numbers of the yeast on cytologic examination of otic exudate. Although cytology has high specificity, it has low sensitivity, resulting in false-negatives and posing a challenge for clinicians to accurately diagnose Malassezia otitis. We developed a quantitative PCR (qPCR) to detect and quantify M. pachydermatis yeasts and validate the method with swabs from external ear canals of dogs. Our qPCR uses the β-tubulin gene, a single-copy gene, as a target. The limit of quantification was established as 0.18 ng/reaction, equivalent to 2.0 × 10⁴ genome equivalents (gEq). Swabs from healthy dogs yielded quantification values of ≤2.7 × 10⁴ gEq in the qPCR, whereas swabs from dogs with otitis yielded quantification values of ≥2.5 × 10⁵ gEq. Our qPCR assay provides accurate quantification of M. pachydermatis yeasts from swab samples from dogs, is more sensitive than cytology, and could be used to monitor response to treatment. Our assay could also be valuable in a research setting to better understand the pathogenesis of M. pachydermatis.

Development of a fluorescence-based method for the rapid determination of Zika virus polymerase activity and the screening of antiviral drugs

Zika virus (ZIKV) is an emerging pathogen that has been associated with large numbers of cases of severe neurologic disease, including Guillain-Barré syndrome and microcephaly. Despite its recent establishment as a serious global public health concern there are no licensed therapeutics to control this virus. Accordingly, there is an urgent need to develop methods for the high-throughput screening of antiviral agents. We describe here a fluorescence-based method to monitor the real-time polymerization activity of Zika virus RNA-dependent RNA polymerase (RdRp). By using homopolymeric RNA template molecules, de novo RNA synthesis can be detected with a fluorescent dye, which permits the specific quantification and kinetics of double-strand RNA formation. ZIKV RdRp activity detected using this fluorescence-based assay positively correlated with traditional assays measuring the incorporation of radiolabeled nucleotides. We also validated this method as a suitable assay for the identification of ZIKV inhibitors targeting the viral polymerase using known broad-spectrum inhibitors. The assay was also successfully adapted to detect RNA polymerization activity by different RdRps, illustrated here using purified RdRps from hepatitis C virus and foot-and-mouth disease virus. The potential of fluorescence-based approaches for the enzymatic characterization of viral polymerases, as well as for high-throughput screening of antiviral drugs, are discussed.

An aptamer based thermofluorimetric assay for ethanolamine

There is a great need for fast, simple and precise diagnostic assays capable of direct quantification of biomarkers in complex biological matrices. Yet, the commonly used techniques such as ELISA/Immunoassays are tedious and involve various steps e.g. blocking, washing and signal development. Moreover, most of these assays have very limited ability of detecting small molecules and have hardly any multiplexing capabilities. The gold standard and alternative, mass-spectrometry, however, depends upon expensive hardware and is incompatible with point of care (POC) diagnostics. As opposed to POC assays for proteins or larger targets where variable formats are readily available. Here, we present a simple, versatile and fast one-step assay for detecting a small molecule, ethanolamine as example. The assay makes use of commonly available qPCR machines to detect target-concentration dependent shifts in the melting temperatures of aptamer beacons. The method allows detection of ethanolamine in the low nM range without requiring tedious elaboration of assay conditions as required for molecular beacons at room temperature. If generalizable, it may change the situation of small molecule assays significantly.

A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus

Respiratory syncytial virus (RSV) causes serious respiratory tract infection worldwide. The relatively low RSV load makes it difficult to detect in frail, elderly, and severely immune-compromised patients. In the present study, we developed a locked nucleic acid–-based 1-tube nested real-time RT-PCR (OTNRT-PCR) assay with the advantages of extremely high sensitivity, facile operability, and less likelihood of cross-contamination. The sensitivity, specificity, and clinical performance of the OTNRT-PCR assay were compared in parallel with a conventional TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional 2-step nested RT-PCR assay. The limit of detection of the OTNRT-PCR assay was 1.02 × 10⁻¹ TCID50/mL, equivalent to the traditional 2-step nested RT-PCR assay and 25-fold lower than the qRT-PCR assay. Of 616 nasopharyngeal aspirates tested, 143 RSV-negative samples by qRT-PCR were confirmed as positive by sequencing the OTNRT-PCR products. We therefore conclude that OTNRT-PCR is more sensitive than qRT-PCR for detection of RSV in clinical samples.

Novel properties of recombinant Sso7d-Taq DNA polymerase purified using aqueous two-phase extraction: Utilities of the enzyme in viral diagnosis

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Sso7d-Taq fusion protein purified using a single step of aqueous Two-Phase Extraction (ATPE) is >95% pure and is active.

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The S-Taq protein has higher thermostability and detergent tolerance over regular Taq polymerase and can be used for PCR's from direct whole blood.

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The PCR efficiency rate of S-Taq is higher than Taq polymerase and can be used to detect DNA viruses in a clinical setting efficiently.

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S-Taq can tolerate higher concentrations of magnesium ions and can be used for in-situ PCR’s.

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S-Taq can be used to carry out PCR’s of bacterial recombinants directly from the overnight culture since it is resistant to inhibition to Luria Bertani broth. This unique property of S-Taq will enable researchers to screen recombinants without the need to isolate the plasmid DNA of recombinants. This would be a huge cost savings for companies engaged in molecular biology research involving PCR’s.

Using Sso7d from Sulfolobus solfataricus as the DNA binding protein fused to Taq DNA polymerase at its amino terminus, we report the hyper-expression and a novel purification methodology of Sso7d-Taq polymerase (S-Taq) using aqueous two-phase extraction system followed by Ni-affinity chromatography. The utility of such a fusion enzyme in carrying out PCR of human genes from whole blood directly and in detecting hepatitis B virus from clinical samples is demonstrated in this article. We present data on the enhanced thermo-stability of S-Taq DNA polymerase over Taq DNA polymerase and also provide evidence of its higher stability with detergents in comparison to Taq polymerase. The purified S-Taq protein showed acceptable limits of host genomic DNA levels without the use of DNases and other DNA precipitating agents and shows promising potential for use in PCR based diagnostics, in-situ PCR’s and forensic science.

A Fast and Reliable Real-Time PCR Method for Detection of Ten Animal Species in Meat Products

Species substitution in meat products is a common problem reported worldwide. This type of food fraud is, typically, an intentional act for economic gain, using sources of low-priced meats in high-value meat products. Consequences include economic, health, and religious concerns. Highly sensitive and efficient techniques are thus required to detect meat species. This paper describes a method based on real-time PCR to detect 10 animal species (Bos taurus, Sus scrofa, Ovis aries, Capra hircus, Gallus gallus, Meleagris gallopavo, Bubalus bubalis, Equus caballus, Felis catus, and Canis familiaris) in meat product. The method combines species-specific and universal (used here as internal positive control) primers, and applies melt curve analysis for amplicon checking. Method accuracy was evaluated on 46 experimental meat mixtures and all species were correctly identified in all cases, at 1% test sensitivity. Analysis of 14 commercial meat products revealed that 6 of 14 samples had nondeclared bovine and/or chicken material. We performed an interlaboratory comparison using the reference meat mixtures and commercial samples, achieving 100% of reproducibility. The developed test proved to be effective and reliable for routine analysis of meat products.

PRACTICAL APPLICATION

This paper describes a fast and reliable method for species detection in meat products based on real-time PCR. It can be applied for analysis of in natura or processed meat. The method proposed here can play an important role in controlling the origin of meat products, ensuring their quality and safety for the entire food industry-producers to consumers.

A novel quantitative PCR mediated by high-fidelity DNA polymerase

The biggest challenge for accurate diagnosis of viral infectious disease is the high genetic variability of involved viruses, which affects amplification efficiency and results in low sensitivity and narrow spectrum. Here, we developed a new simple qPCR mediated by high-fidelity (HF) DNA polymerase. The new method utilizes an HFman probe and one primer. Fluorescent signal was generated from the 3'-5' hydrolysis of HFman probe by HF DNA polymerase before elongation initiation. Mismatches between probe/primer and template have less influence on the amplification efficiency of the new method. The new qPCR exhibited higher sensitivity and better adaptability to sequence variable templates than the conventional TaqMan probe based-qPCR in quantification of HIV-1 viral load. Further comparison with COBAS TaqMan HIV-1 Test (v2.0) showed a good correlation coefficient (R² = 0.79) between both methods in quantification of HIV-1 viral load among 21 clinical samples. The characteristics of tolerance to variable templates and one probe-one primer system imply that the probe/primer design for the new method will be easier and more flexible than the conventional method for highly heterogeneous viruses. Therefore, the HF DNA polymerase-mediated qPCR method is a simple, sensitive and promising approach for the development of diagnostics for viral infectious diseases.

High-Resolution Melting Analysis for Rapid Detection of Sequence Type 131 Escherichia coli

Escherichia coli isolates belonging to the sequence type 131 (ST131) clonal complex have been associated with the global distribution of fluoroquinolone and β-lactam resistance. Whole-genome sequencing and multilocus sequence typing identify sequence type but are expensive when evaluating large numbers of samples. This study was designed to develop a cost-effective screening tool using high-resolution melting (HRM) analysis to differentiate ST131 from non-ST131 E. coli in large sample populations in the absence of sequence analysis. The method was optimized using DNA from 12 E. coli isolates. Singleplex PCR was performed using 10 ng of DNA, Type-it HRM buffer, and multilocus sequence typing primers and was followed by multiplex PCR. The amplicon sizes ranged from 630 to 737 bp. Melt temperature peaks were determined by performing HRM analysis at 0.1°C resolution from 50 to 95°C on a Rotor-Gene Q 5-plex HRM system. Derivative melt curves were compared between sequence types and analyzed by principal component analysis. A blinded study of 191 E. coli isolates of ST131 and unknown sequence types validated this methodology. This methodology returned 99.2% specificity (124 true negatives and 1 false positive) and 100% sensitivity (66 true positives and 0 false negatives). This HRM methodology distinguishes ST131 from non-ST131 E. coli without sequence analysis. The analysis can be accomplished in about 3 h in any laboratory with an HRM-capable instrument and principal component analysis software. Therefore, this assay is a fast and cost-effective alternative to sequencing-based ST131 identification.

Stem loop-mediated isothermal amplification test: comparative analysis with classical LAMP and PCR in detection of Entamoeba histolytica in Kenya

BACKGROUND

Entamoeba histolytica, the causative agent for amoebiasis is a considerable burden to population in the developing countries where it accounts for over 50 million infections. The tools for detection of amoebiasis are inadequate and diagnosis relies on microscopy which means a significant percent of cases remain undiagnosed. Moreover, tests formats that can be rapidly applied in rural endemic areas are not available.

METHODS

In this study, a loop-mediated isothermal test (LAMP) based on 18S small subunit ribosomal RNA gene was designed with extra reaction accelerating primers (stem primers) and compared with the published LAMP and PCR tests in detection of E. histolytica DNA in clinical samples.

RESULTS

The stem LAMP test indicated shorter time to results by an average 11 min and analytical sensitivity of 10^-7 (~30 pg/ml) compared to the standard LAMP and PCR which showed sensitivities levels of 10^-5 (~3 ng/ml) and 10^-4 (~30 ng/ml) respectively using tenfold serial dilution of DNA. In the analysis of clinical specimens positive for Entamoeba spp. trophozoites and cysts using microscopy, the stem LAMP test detected E. histolytica DNA in 36/126, standard LAMP test 20/126 and PCR 17/126 cases respectively. There was 100% agreement in detection of the stem LAMP test product using fluorescence of SYTO-9 dye in real time machine, through addition of 1/10 dilution of SYBR^® Green I and electrophoresis in 2% agarose gel stained with ethidium bromide.

CONCLUSION

The stem LAMP test developed in this study indicates potential towards detection of E. histolytica.

Highly Stable and Sensitive Nucleic Acid Amplification and Cell-Phone-Based Readout

Key challenges with point-of-care (POC) nucleic acid tests include achieving a low-cost, portable form factor, and stable readout, while also retaining the same robust standards of benchtop lab-based tests. We addressed two crucial aspects of this problem, identifying a chemical additive, hydroxynaphthol blue, that both stabilizes and significantly enhances intercalator-based fluorescence readout of nucleic acid concentration, and developing a cost-effective fiber-optic bundle-based fluorescence microplate reader integrated onto a mobile phone. Using loop-mediated isothermal amplification on lambda DNA we achieve a 69-fold increase in signal above background, 20-fold higher than the gold standard, yielding an overall limit of detection of 25 copies/μL within an hour using our mobile-phone-based platform. Critical for a point-of-care system, we achieve a >60% increase in fluorescence stability as a function of temperature and time, obviating the need for manual baseline correction or secondary calibration dyes. This field-portable and cost-effective mobile-phone-based nucleic acid amplification and readout platform is broadly applicable to other real-time nucleic acid amplification tests by similarly modulating intercalating dye performance and is compatible with any fluorescence-based assay that can be run in a 96-well microplate format, making it especially valuable for POC and resource-limited settings.

Development of a multiplex real-time PCR assay for phylogenetic analysis of Uropathogenic Escherichia coli

Uropathogenic Escherichia coli (UPEC) is among major pathogens causing 80-90% of all episodes of urinary tract infections (UTIs). Recently, E. coli strains are divided into eight main phylogenetic groups including A, B1, B2, C, D, E, F, and clade I. This study was aimed to develop a rapid, sensitive, and specific multiplex real time PCR method capable of detecting phylogenetic groups of E. coli strains. This study was carried out on E. coli strains (isolated from the patient with UTI) in which the presence of all seven target genes had been confirmed in our previous phylogenetic study. An EvaGreen-based singleplex and multiplex real-time PCR with melting curve analysis was designed for simultaneous detection and differentiation of these genes. The primers were selected mainly based on the production of amplicons with melting temperatures (T_m) ranging from 82°C to 93°C and temperature difference of more than 1.5°C between each peak.The multiplex real-time PCR assays that have been developed in the present study were successful in detecting the eight main phylogenetic groups. Seven distinct melting peaks were discriminated, with Tm value of 93±0.8 for arpA, 89.2±0.1for chuA, 86.5±0.1 for yjaA, 82.3±0.2 for TspE4C2, 87.8±0.1for trpAgpC, 85.4±0.6 for arpAgpE genes, and 91±0.5 for the internal control. To our knowledge, this study is the first melting curve-based real-time PCR assay developed for simultaneous and discrete detection of these seven target genes. Our findings showed that this assay has the potential to be a rapid, reliable and cost-effective alternative for routine phylotyping of E. coli strains.

Identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by righ-resolution melting analysis

The objective of this study was to standardize the high-resolution melting method for identification and discrimination of Toxoplasma gondii, Sarcocystis spp., Neospora spp., and Cryptosporidium spp. by amplification of 18S ribosomal DNA (rDNA) using a single primer pair. The analyses were performed on individual reactions (containing DNA from a single species of a protozoan), on duplex reactions (containing DNA from two species of protozoa in each reaction), and on a multiplex reaction (containing DNA of four parasites in a single reaction). The proposed method allowed us to identify and discriminate the four species by analyzing the derivative, normalized, and difference melting curves, with high reproducibility among and within the experiments, as demonstrated by low coefficients of variation (less than 2.2% and 2.0%, respectively). This is the first study where this method is used for discrimination of these four species of protozoa in a single reaction.

Loop-Mediated Isothermal Amplification Test for Trypanosoma gambiense Group 1 with Stem Primers: A Molecular Xenomonitoring Test for Sleeping Sickness

The World Health Organization has targeted Human African Trypanosomiasis (HAT) for elimination by 2020 with zero incidence by 2030. To achieve and sustain this goal, accurate and easy-to-deploy diagnostic tests for Gambian trypanosomiasis which accounts for over 98% of reported cases will play a crucial role. Most needed will be tools for surveillance of pathogen in vectors (xenomonitoring) since population screening tests are readily available. The development of new tests is expensive and takes a long time while incremental improvement of existing technologies that have potential for xenomonitoring may offer a shorter pathway to tools for HAT surveillance. We have investigated the effect of including a second set of reaction accelerating primers (stem primers) to the standard T. brucei gambiense LAMP test format. The new test format was analyzed with and without outer primers. Amplification was carried out using Rotorgene 6000 and the portable ESE Quant amplification unit capable of real-time data output. The stem LAMP formats indicated shorter time to results (~8 min), were 10–100-fold more sensitive, and indicated higher diagnostic sensitivity and accuracy compared to the standard LAMP test. It was possible to confirm the predicted product using ESE melt curves demonstrating the potential of combining LAMP and real-time technologies as possible tool for HAT molecular xenomonitoring.

Application of unique sequence index (USI) barcode to gene expression profiling in gastric adenocarcinoma

Accurate expression profiling is imperative for understanding the biological roles of mRNAs. Real-time PCR have been at the forefront of biological innovation in detection and monitoring of gene expression, however, fluorophore-labeled oligonucleotides and double-stranded DNA binding dyes, the two most frequently used dyes in RNA detection, are not very cost effective and have poor specificity, respectively. We have developed a cost effective and specific approach for mRNA expression profiling via added unique sequence index (USI) to cDNAs before amplification. USI is a barcode which enable the detection of each target RNA. Using this method, caudal type homeobox 1 (CDX1) and FAT atypical cadherin 4 (FAT4) expressions were investigated in tumoral and non-tumoral tissues of gastric cancer patients and compared with commercial ABI kit. Both methods indicated that FAT4 and CDX1 expression were significantly reduced in gastric cancer tissues compared with adjacent noncancerous tissues. Moreover, we have shown that this assay is highly sensitive, linear and reproducible. USI barcode not only provides a powerful tool for mRNA detection due to its sensitivity, specificity and cost-effectiveness, but also allows comfortable design for real-time qPCR assays within the least time and empowers the analysis of many transcripts of virtually any organism. Furthermore, USI barcode is highly affordable for large numbers of different samples or small sample sizes without microarray and expensive commercial platforms.

High-Throughput Genotyping with TaqMan Allelic Discrimination and Allele-Specific Genotyping Assays

Real-time PCR-based genotyping methods, such as TaqMan allelic discrimination assays and allele-specific genotyping, are particularly useful when screening a handful of single nucleotide polymorphisms in hundreds of samples; either derived from different individuals, tissues, or pre-amplified DNA. Although real-time PCR-based methods such as TaqMan are well-established, alternative methods, like allele-specific genotyping, are powerful alternatives, especially for genotyping short tandem repeat (STR) length polymorphisms. Here, we describe all relevant aspects when developing an assay for a new SNP or STR using either TaqMan or allele-specific genotyping, respectively, such as primer and probe design, optimization of reaction conditions, the experimental procedure for typing hundreds of samples, and finally the data evaluation. Our goal is to provide a guideline for developing genotyping assays using these two approaches that render reliable and reproducible genotype calls involving minimal optimization.

A Melting Curve-Based Multiplex RT-qPCR Assay for Simultaneous Detection of Four Human Coronaviruses

Human coronaviruses HCoV-OC43, HCoV-229E, HCoV-NL63 and HCoV-HKU1 are common respiratory viruses associated with acute respiratory infection. They have a global distribution. Rapid and accurate diagnosis of HCoV infection is important for the management and treatment of hospitalized patients with HCoV infection. Here, we developed a melting curve-based multiplex RT-qPCR assay for simultaneous detection of the four HCoVs. In the assay, SYTO 9 was used to replace SYBR Green I as the fluorescent dye, and GC-modified primers were designed to improve the melting temperature (Tm) of the specific amplicon. The four HCoVs were clearly distinguished by characteristic melting peaks in melting curve analysis. The detection sensitivity of the assay was 3 × 10² copies for HCoV-OC43, and 3 × 10¹ copies for HCoV-NL63, HCoV-229E and HCoV-HKU1 per 30 μL reaction. Clinical evaluation and sequencing confirmation demonstrated that the assay was specific and reliable. The assay represents a sensitive and reliable method for diagnosis of HCoV infection in clinical samples.

Poisonous or non-poisonous plants? DNA-based tools and applications for accurate identification

Plant exposures are among the most frequently reported cases to poison control centres worldwide. This is a growing condition due to recent societal trends oriented towards the consumption of wild plants as food, cosmetics, or medicine. At least three general causes of plant poisoning can be identified: plant misidentification, introduction of new plant-based supplements and medicines with no controls about their safety, and the lack of regulation for the trading of herbal and phytochemical products. Moreover, an efficient screening for the occurrence of plants poisonous to humans is also desirable at the different stages of the food supply chain: from the raw material to the final transformed product. A rapid diagnosis of intoxication cases is necessary in order to provide the most reliable treatment. However, a precise taxonomic characterization of the ingested species is often challenging. In this review, we provide an overview of the emerging DNA-based tools and technologies to address the issue of poisonous plant identification. Specifically, classic DNA barcoding and its applications using High Resolution Melting (Bar-HRM) ensure high universality and rapid response respectively, whereas High Throughput Sequencing techniques (HTS) provide a complete characterization of plant residues in complex matrices. The pros and cons of each approach have been evaluated with the final aim of proposing a general user's guide to molecular identification directed to different stakeholder categories interested in the diagnostics of poisonous plants.