Copies μL-1 Research Articles

Simultaneous enumeration of Cronobacter sakazakii and Staphylococcus aureus in powdered infant foods through duplex TaqMan real-time PCR

Cronobacter sakazakii and Staphylococcus aureus are important pathogens. Targeting the species-specific macromolecular synthesis (MMS) operon and thermostable nuclease gene (nuc), a duplex TaqMan real-time PCR (dRT-PCR) assay was developed for their simultaneous enumeration within two kinds of powdered infant foods (PIFs). The assay was highly specific, producing fluorescent signals exclusively from target bacteria. The quantification limits were 29.10 and 8.97 copies μL−1 for standard plasmids containing MMS and nuc fragments. Without enrichment, the dRT-PCR could quantify as low as 102 and 101 cfu mL−1C. sakazakii and S. aureus in both pure culture and spiked PIFs. Quantitative linearity ranged from 102 to 107 cfu mL−1 for C. sakazakii and from 101 to 107 cfu mL−1 for S. aureus. Bacterial counts derived from dRT-PCR were consistent with those calculated from plating for randomly spiked PIFs. The dRT-PCR assay provides a promising culture-independent alternative enabling direct, simultaneous and robust pathogen quantification.

Is there bacterial infection in the intact crowns of teeth with pulp necrosis of sickle cell anaemia patients? A case series study nested in a cohort.

To evaluate the presence of bacteria in permanent teeth with intact crowns (without caries, periodontal disease or dental trauma) in patients with sickle cell anaemia (HbSS genotype) by analysing their clinical, imaging and microbiological parameters. This is a case series study nested in a cohort. In the first follow-up of this cohort study (Journal of Endodontics, 2013, 39, 177), 10 HbSS patients with at least one tooth with an intact crown and clinically diagnosed with pulp necrosis by pulse oximetry adapted for dentistry and a cold pulp sensitivity test (n=27 teeth) were selected. Changes in the pulp chamber, root and periodontal ligament were identified in the tomographic analysis. Bacterial culture, staining for live and dead bacteria, and real-time polymerase chain reaction with 16S rRNA primers were used to identify the presence of bacteria. Culture sample collection was performed immediately after access to the pulp chamber. The microbiome was analysed with a MiSeq sequencer (Illumina, San Diego, CA). The diagnosis of pulp necrosis was confirmed clinically in 82% (22/27) of the teeth. The amount of bacterial load identified was less than 100copiesμL-1 in 23% (5/22) of the teeth with intact crowns and pulp necrosis. Thirteen bacterial species were identified that are commonly found in urinary tract infections, septicaemia and infective endocarditis. Only one of these species, Granulicatella adjacens, has also be found in primary endodontic infections. Prospective clinical, imaging and microbiological analyses suggest that pulp necrosis of teeth with intact crowns in HbSS patients is not associated with the presence of bacteria.

Hairpin-Structured Magnetic SERS Sensor for Tetracycline Resistance Gene tetA Detection.

Antibiotic resistance genes (ARGs) have become emerging environmental contaminants, and the effective on-site detection of ARGs is urgently needed. Herein, we constructed a hairpin-structured magnetic sensor for the analysis of a widespread ARG, tetA, using surface-enhanced Raman scattering (SERS). The SERS sensor was assembled by immobilizing core-satellite structured Fe3O4@SiO2-Au with single-stranded DNA in a folded hairpin structure. The SERS sensor exhibited good sensitivity and specificity for the detection of laboratory-synthesized tetA ssDNA fragments. In addition, this SERS strategy is the first of its kind to be employed for monitoring environmental samples in the field, with a limit of detection reaching as low as 25 copies μL-1. Univariate and multivariate linear regression equations verify the practicability of the SERS sensor for quantitative tetA determination, showing the prospect for an amplification-free alternative platform for sensitive and reliable on-site detection of ARGs in the environment.

Development of a recombinase polymerase amplification (RPA-EXO) and lateral flow assay (RPA-LFA) based on the ITS1 gene for the detection of Angiostrongylus cantonensis in gastropod intermediate hosts.

Angiostrongylus cantonensis is a parasitic nematode known to infect humans through the ingestion of third stage larvae which can cause inflammation and damage to the central nervous system. Currently, polymerase chain reaction (PCR) is one of the most reliable diagnostic methods for detecting A. cantonensis in humans as well as in gastropod hosts, but requires expensive and specialized equipment. Here, we compare the sensitivity and accuracy of a recombinase polymerase amplification Exo (RPA-EXO) assay, and a recombinase polymerase amplification lateral flow assay (RPA-LFA) with a traditional quantitative PCR (qPCR) assay currently available. The three assays were used to test 35 slugs from Hawai'i for the presence of A. cantonensis DNA. Consistent results among the three tests were shown in 23/35 samples (65.7%), while 7/35 (20%) were discordant in low infection level samples (<0.01 larvae per mg tissue), and 5/35 (14.3%) were equivocal. To evaluate sensitivity, a partial ITS1 gene was cloned, and serial plasmid dilutions were created ranging from 100 copies μL-1 to ~1 copy μL-1. All three assays consistently detected 50-100 copies μL-1 in triplicate and qPCR was able to detect ~13 copies μL-1 in triplicate. RPA-EXO was able to detect 25 copies μL-1 in triplicate and RPA-LFA was not able to amplify consistently below 50 copies μL-1. Thus, our RPA-EXO and RPA-LFA assays do not appear as sensitive as the current qPCR assay at low DNA concentrations; however, these tests have numerous advantages that may make them useful alternatives to qPCR.

Rapid, Ultrasensitive, and Quantitative Detection of SARS-CoV-2 Using Antisense Oligonucleotides Directed Electrochemical Biosensor Chip.

A large-scale diagnosis of the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) is essential to downregulate its spread within as well as across communities and mitigate the current outbreak of the pandemic novel coronavirus disease 2019 (COVID-19). Herein, we report the development of a rapid (less than 5 min), low-cost, easy-to-implement, and quantitative paper-based electrochemical sensor chip to enable the digital detection of SARS-CoV-2 genetic material. The biosensor uses gold nanoparticles (AuNPs), capped with highly specific antisense oligonucleotides (ssDNA) targeting viral nucleocapsid phosphoprotein (N-gene). The sensing probes are immobilized on a paper-based electrochemical platform to yield a nucleic-acid-testing device with a readout that can be recorded with a simple hand-held reader. The biosensor chip has been tested using samples collected from Vero cells infected with SARS-CoV-2 virus and clinical samples. The sensor provides a significant improvement in output signal only in the presence of its target—SARS-CoV-2 RNA—within less than 5 min of incubation time, with a sensitivity of 231 (copies μL–1)−1 and limit of detection of 6.9 copies/μL without the need for any further amplification. The sensor chip performance has been tested using clinical samples from 22 COVID-19 positive patients and 26 healthy asymptomatic subjects confirmed using the FDA-approved RT-PCR COVID-19 diagnostic kit. The sensor successfully distinguishes the positive COVID-19 samples from the negative ones with almost 100% accuracy, sensitivity, and specificity and exhibits an insignificant change in output signal for the samples lacking a SARS-CoV-2 viral target segment (e.g., SARS-CoV, MERS-CoV, or negative COVID-19 samples collected from healthy subjects). The feasibility of the sensor even during the genomic mutation of the virus is also ensured from the design of the ssDNA-conjugated AuNPs that simultaneously target two separate regions of the same SARS-CoV-2 N-gene.

Rapid detection of Pseudomonas aeruginosa by cross priming amplification

Pseudomonas aeruginosa (PA) is an opportunistic pathogen of humans and animals and a common source of nosocomial infections especially of the respiratory tract. Pseudomonas aeruginosa is also a major bacterial disease of poultry and in particular, eggs and newly hatched chicks. In this study, we developed a simple, accurate and rapid molecular detection method using cross priming amplification (CPA) with a nucleic acid test strip to detect P. aeruginosa. The assay efficiently amplified the target gene within 45 min at 62°C only using a simple water bath. The detection limit of the method was 1.18×102 copies μL−1 for plasmid DNA and 4.4 CFU mL−1 for bacteria in pure culture, and was 100 times more sensitive than conventional PCR. We screened 83 clinical samples from yellow-feather broiler breeder chickens and hospitalized/treated dogs and cats using CPA, PCR and traditional culture methods. The positive-sample ratios were 15.3% (13/83) by CPA, 13.3% (11/83) by PCR and 12.1% (10/83) by the culture method. The established CPA method has significant advantages for detecting P. aeruginosa. The method is easy to use and possesses high specificity and sensitivity without the requirements of complicated experimental equipment. The PA-CPA assay is especially fit for outdoor and primary medical units and is an ideal system for the rapid detection and monitoring of P. aeruginosa.

Development of a rapid screening test for Karenia mikimotoi by using loop-mediated isothermal amplification and lateral flow dipstick

As a bloom-forming dinoflagellate, Karenia mikimotoi is toxic and globally distributed. Frequent outbreaks of K. mikimotoi blooms usually lead to the mass mortality of pelagic and benthic marine life, resulting in large economic losses. Therefore, the simple, rapid, and highly effective monitoring of K. mikimotoi is crucial to minimize the damage caused by this alga. This study aimed to establish a convenient, cost-effective, and efficient molecular detection technique through loop-mediated isothermal amplification (LAMP) combined with chromatographic lateral flow dipstick (LFD) for the daily monitoring and real-time detection of K. mikimotoi. The internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequences of K. mikimotoi were used to design and screen an optimal primer (KmLF3) and a detection probe (KmLF3HP). The optimized LAMP conditions were as follows: dNTP concentration, 1.2 mM; betaine concentration, 1 M; ratio of the inner primer to the outer primer, 8:1; magnesium ion concentration, 8 mM; amplification temperature, 59 °C; and amplification time, 60 min. Cross-reactivity tests confirmed the specificity of LAMP–LFD. The detection limit of LAMP–LFD for K. mikimotoi genomic DNA was 1.70 × 10−4 ng μL−1, which is 100 times lower than that of conventional PCR. The detection limit of LAMP–LFD for the recombinant plasmid containing the LSU rDNA of K. mikimotoi was 6.21 × 103 copies μL−1, which was 10 times more sensitive than that of LAMP followed by agarose gel electrophoresis and SYBR Green I dye staining and 100 times lower than that of conventional PCR. The practicability of LAMP–LFD was validated by testing with simulated field-water samples, displaying a detection limit of 10−1 cells mL−1. In conclusion, the developed LAMP–LFD is a specific, sensitive, and accurate detection method and may be competent for the field detection of K. mikimotoi.

A photoelectrochemical biosensor for rapid and ultrasensitive norovirus detection

The highly contagious norovirus (NoV) is the most common causative agent of acute gastroenteritis, resulting in >200,000 deaths worldwide annually. A rapid and sensitive detection method is a prerequisite for effective prevention and timely identification of NoV contamination. In the present study, we developed a photoelectrochemical (PEC) biosensor coupled with a novel custom-made monoclonal antibody (mAb) for specific and sensitive NoV detection. Our system could detect levels of recombinant NoV capsid protein VP1 as low as 2 × 10−10 g mL−1 (4.9 pM) within 30 min in a concentration-dependent manner. More importantly, the biosensor was versatile in detecting virus isolated from real samples that were as low as 46 copies μL−1. These findings indicate that this system has the potential to serve as a convenient point-of-care system for diagnosing NoV infection and detecting NoV-contaminated food samples.

Establishment of double probes rolling circle amplification combined with lateral flow dipstick for rapid detection of Chattonella marina

Chattonella marina is one of the main algae that could cause harmful algal blooms. It has killed a large number of cultured fish in coastal areas of many countries, causing serious economic losses. Therefore, it is necessary to establish a method that can specifically detect C. marina at pre-bloom abundance, so that timely measures can be taken before this alga causes harm. In this study, a long probe, a short probe and a pair of amplification primers were first designed by using the internal transcribed spacer (ITS) sequence of C. marina as the target gene and using the CD74 gene of a distant species Gallus gallus as the base sequence. The double probes rolling circle amplification (dpRCA) system was then established with the designed probes and amplification primers. A novel detection protocol referred to as dpRCA-LFD by combining the dpRCA products and lateral flow dipstick (LFD) was finally established, which can make the detection results visible to the naked eyes. The reaction conditions of dpRCA were optimized and the optimal conditions were as follows: cycle number of ligation reaction, 12; ligation temperature, 58 °C; amplification temperature, 60 °C; and amplification time, 60 min. The specificity test that was performed using the optimized dpRCA conditions indicated that dpRCA-LFD was exclusively specific for the target alga. The tests with the genomic DNA of C. marina and the recombinant plasmid containing the ITS sequence of C. marina showed that the sensitivity of dpRCA-LFD was 100 times higher than that of conventional PCR. The detection limit (DL) for the genomic DNA was 8.3 × 10−3 ng µL−1 (8.3 × 10−3 ng per reaction), and the DL for the recombinant plasmid DNA was 7.8 copies µL−1 (7.8 copies per reaction). The practicality of the developed dpRCA-LFD was further validated by test with the spiked samples containing C. marina and field samples. The simulative test showed that the dpRCA-LFD has a DL of 10 cells mL−1. The dpRCA-LFD could successfully recognize the target cells from the field samples. In summary, the dpRCA-LFD established in this study has advantages of good specificity, high sensitivity, and easily visible detection results, and therefore is promising for the analysis of C. marina in field samples.

Reliable eDNA detection and quantification of the European weather loach (Misgurnus fossilis).

The European weather loach (Misgurnus fossilis) is a cryptic and poorly known fish species of high conservation concern. The species is experiencing dramatic population collapses across its native range to the point of regional extinction. Although environmental DNA (eDNA)-based approaches offer clear advantages over conventional field methods for monitoring rare and endangered species, accurate detection and quantification remain difficult and quality assessment is often poorly incorporated. In this study, we developed and validated a novel digital droplet PCR (ddPCR) eDNA-based method for reliable detection and quantification, which allows accurate monitoring of M. fossilis across a number of habitat types. A dilution experiment under laboratory conditions allowed the definition of the limit of detection (LOD) and the limit of quantification (LOQ), which were set at concentrations of 0.07 and 0.14 copies μl-1 , respectively. A series of aquarium experiments revealed a significant and positive relationship between the number of individuals and the eDNA concentration measured. During a 3 year survey (2017-2019), we assessed 96 locations for the presence of M. fossilis in Flanders (Belgium). eDNA analyses on these samples highlighted 45% positive detections of the species. On the basis of the eDNA concentration per litre of water, only 12 sites appeared to harbour relatively dense populations. The other 31 sites gave a relatively weak positive signal that was typically situated below the LOQ. Combining sample-specific estimates of effective DNA quantity (Qe ) and conventional field sampling, we concluded that each of these weak positive sites still likely harboured the species and therefore they do not represent false positives. Further, only seven of the classified negative samples warrant additional sampling as our analyses identified a substantial risk of false-negative detections (i.e., type II errors) at these locations. Finally, we illustrated that ddPCR outcompetes conventional qPCR analyses, especially when target DNA concentrations are critically low, which could be attributed to a reduced sensitivity of ddPCR to inhibition effects, higher sample concentrations being accommodated and higher sensitivity obtained.

Application of the novel Droplet digital PCR technology for identification of meat species

AbstractThe authenticity and traceability of meat products are issues of primary importance to ensure food safety. Unfortunately, food adulteration (e.g. the addition of inexpensive cuts to minced meat products) and mislabelling (e.g. the inclusion of meat from species other than those declared) happens frequently worldwide. The aim of this study was to apply a droplet digital PCR assay for the detection and quantification (copies μL−1) of the beef, pork, horse, sheep, chicken and turkey in meat products. The analysis conducted on commercial meat showed the presence of traces of DNA from other animal species than those declared. We show that the method is highly sensitive, specific and accurate (accuracy = 100%). This method could be adopted by competent food safety authorities to verify compliance with the labelling of meat products and to ensure quality and safety throughout the meat supply chain, from primary production to consumption.

Prevalence of Aeromonas hydrophila and Pseudomonas fluorescens and factors influencing them in different freshwater fish ponds

Real-time quantitative PCR (qPCR) was performed to elucidate the abundance of Aeromonas hydrophila and Pseudomonas fluorescens, which are among the most widespread fish pathogens in ponds. Both pathogens have three different breeding patterns, namely, (a) gibel carp (Carassius auratus gibelio), (b) yellow catfish (Pelteobagrus fulvidraco), and (c) black carp (Mylopharyngodon piceus), over a production season. Results revealed that pond sediments have significantly higher bacterial levels of A. hydrophila and P. fluorescens (105–106 copies µl-1 DNA) than pond water (103–104 copies µl-1 DNA). In addition, independent regression models revealed that environmental variables influence the levels of pathogenic bacteria. The occurrence of A. hydrophila and P. fluorescens were significantly positively correlated to dissolved oxygen and water temperature, respectively. On the contrary, both pathogens were negatively correlated to total nitrogen. In this study, the prevalence of pathogenic bacteria and their relationships with physicochemical factors in different pond environments were investigated for the first time through a molecular method. Furthermore, although we did not include fish diseases occurring during the production season, our results can provide useful theoretical information for fish breeding especially with regard to the prevention of related bacterial diseases.

Application of loop-mediated isothermal amplification combined with lateral flow dipstick to rapid and sensitive detection of Alexandrium catenella.

Alexandrium catenella is one of the globally distributed toxic marine microalgae to cause paralytic shellfish poisoning that poses a great threat to marine fisheries, economy, and public health. Development of efficient and sensitive methods for accurate identification of A. catenella to minimize its damage is therefore necessary. In this study, a novel method referred to as loop-mediated isothermal amplification (LAMP) combined with lateral flow dipstick (LFD) (LAMP-LFD) was established for rapid and sensitive detection of A. catenella. The internal transcribed spacer (ITS) gene of A. catenella was cloned for sequencing and used as target for LAMP-LFD. Three sets of LAMP primers (AcLF1, AcLF2, and AcLF3) targeting the ITS were successfully designed, among which AcLF2 displaying the best performance was used in the subsequent tests. A specific LFD probe targeting the amplification region of AcLF2 was further designed. The LAMP-LFD detection system was established and the amplification conditions were optimized. Cross-reactivity tests with common marine microalgae showed that the LAMP-LFD was exclusively specific for A. catenella. The detection limits of LAMP-LFD for A. catenella genomic DNA and the plasmid containing the ITS were 4.63 × 10-4 ng μL-1 and 1.26 × 104 copies μL-1, displaying a sensitivity that is 10 times higher than that of SYBR Green I assay and 100 times higher than that of conventional PCR, respectively. Finally, the practicability of LAMP-LFD was confirmed by test with spiked samples. LAMP-LFD revealed a detection limit of approximately 0.1 cell mL-1, which was 100 times more sensitive than conventional PCR. The optimized LAMP-LFD protocol can be completed within 75 min. Therefore, the established LAMP-LFD is a specific, sensitive, and rapid method that is possibly applicable to the field monitoring of A. catenella.

Development and Application of a Real-Time Reverse-Transcription PCR and Droplet Digital PCR Assays for the Direct Detection of Potato mop top virus in Soil.

Potato mop top virus (PMTV) is a continuing threat to potato production throughout the world. It has the potential to persist in the soil for long periods in the sporosori of its vector Spongospora subterranea f. sp. subterranea, which is as an important source for PMTV infection and dissemination. In this study, we used real-time quantitative reverse-transcription PCR (qRT-PCR) and reverse-transcription droplet digital PCR (RT-ddPCR) assays of the total RNA extracted directly from the soil to develop a simple, fast, and sensitive method to detect PMTV in soil samples using a specific primer with high efficiency despite a minimal amount of viral RNA. The designed primers are resilient in the presence of various PCR inhibitors in the soil when RNA is extracted. Both assays detected PMTV in all soil types used and supported the detection of <10 PMTV copies µl-1 in the RNA sample. With qRT-PCR, detection was linear, with amplification efficiencies ranging from 93.3 to 105.3% for silt loam, loamy sand, sand, and sandy loam in various experiments with R2 > 0.99. Furthermore, the RT-ddPCR assay also demonstrated a high degree of linearity (R2 > 0.99 and P < 0.0001) with the RNA extracted from the soil samples representing different textures and physiochemical characteristics that were artificially spiked with infested S. subterranea f. sp. subterranea sporosori. Additionally, both assays successfully detected PMTV in different types of naturally infested soil with PMTV carrying S. subterranea f. sp. subterranea sporosori levels ranging from 6.2 × 102 g-1 to 1.2 × 106 g-1 in soils with pH ranging from 4.9 to 7.5 and organic matter ranging from 0.9 to 5.1%, demonstrating the potential to detect PMTV in a wide variety of soils. To our knowledge, this is the first report of the development of real-time PCR and ddPCR methods for the direct detection of a soilborne virus in soil.

Probe-Based Multiplex Real-Time PCR as a Diagnostic Tool to Distinguish Distinct Fungal Symbionts Associated With Euwallacea kuroshio and Euwallacea whitfordiodendrus in California.

California has been invaded by two distinct Euwallacea spp. that vector unique plant pathogenic symbiotic fungi on multiple hosts and cause Fusarium dieback. The objective of this study was to develop multiplex real-time quantitative PCR assays using hydrolysis probes targeting the β-tubulin gene to detect, distinguish, and quantify fungi associated with the polyphagous shot hole borer (PSHB; Euwallacea whitfordiodendrus, Fusarium euwallaceae, Graphium euwallaceae, and Paracremonium pembeum) as well as the Kuroshio shot hole borer (KSHB; Euwallacea kuroshio, Fusarium kuroshium, and Graphium kuroshium) from various sample types. Absolute quantification reaction efficiencies ranged from 88.2 to 104.3%, with a coefficient of determination >0.992 and a limit of detection of 100 copies µl-1 for all targets across both assays. Qualitative detection using the real-time assays on artificially inoculated avocado shoot extracts showed more sensitivity compared with conventional fungal isolation from wood. All symbiotic fungi, except P. pembeum, from PSHB and KSHB female heads were detectable and quantified. Field samples from symptomatic Platanus racemosa, Populus spp., and Salix spp. across 17 of 26 city parks were positively identified as PSHB and KSHB through detection of their symbiotic fungi, and both were found occurring together on five trees from three different park locations. The molecular assays presented here can be utilized to accurately identify fungi associated with these invasive pests in California.

Development of loop-mediated isothermal amplification combined with a chromatographic lateral-flow dipstick for rapid detection of Chattonella marina

Harmful algal blooms caused by Chattonella marina recently have caused severe negative effect on coastal economy worldwide, with increased occurrence frequency and scale. It is therefore vital to establish new methods for rapid detection of this alga. In this study, the internal transcribed spacer (ITS) sequence was used as the target gene for molecular detection of C. marina. First, four loop-mediated isothermal amplification (LAMP) primers were designed based on the six regions of ITS, and the LAMP reaction system was established using these primers. Next, a probe was designed to detect the LAMP products by lateral-flow dipstick (LFD). Finally, a new method for rapid and sensitive detection of C. marina that is referred to as LAMP-LFD was established. The LAMP reaction system, amplification time, and amplification temperature were particularly optimized. The optimal parameters are as follows: Mg2+ concentration, 10 mM；dNTP concentration, 1.2 mM；ratio of internal primer concentration to outer primer concentration, 8:1；reaction time, 60 min；and reaction temperature, 60 °C. Both specificity and sensitivity were tested using the optimized LAMP reaction system in combination with LFD (LAMP-LFD). The established LAMP-LFD displayed good specificity and no cross reaction was detected with non-target algal species. The detection limit of LAMP-LFD was 3.4 × 10−4 ng μL−1 (3.4 × 10−4 ng per reaction) for the genomic DNA of target algae, and 1.3 copies μL−1 (1.3 copies per reaction) for the plasmid DNA containing the target ITS. Sensitivity tests using genomic DNA and plasmid DNA as templates consistently revealed that LAMP-LFD is 100 times more sensitive than regular PCR. The established LAMP-LFD was applied to analyze the simulated samples and the results showed that the detection limit of LAMP-LFD could reach 1 cell mL−1. LAMP-LFD also demonstrated good specificity and sensitivity in the analysis of natural samples. The whole procedure of LAMP-LFD could be completed within 1.5 h. Taken together, the LAMP-LFD assay developed here is characterized by simplicity, high specificity and sensitivity, and rapidity and therefore is promising for rapid detection of C. marina.

Linker-protein G mediated functionalization of polystyrene-encapsulated upconversion nanoparticles for rapid gene assay using convective PCR.

The authors report on a simplified approach to encapsulate upconversion nanoparticles (UCNPs) in polystyrene spheres by mini-emulsion polymerisation. The resulting particles (PS-UCNP) are hydrophilic, stable and suitable for biomolecular recognition and biosensing applications. Also, a strategy was developed for bioconjugation of antibodies onto the surface of the PS-UCNPs by using the bifunctional fusion protein linker-protein G (LPG). LPG mediates the functionalisation of PS-UCNPs with antibodies against digoxigenin allowing for specific labelling of convective PCR (cPCR) amplicons. Lambda DNA was amplified using cPCR on a heat block for 30min using the digoxigenin labelled forward and biotin labelled reverse primers. The antibody functionalised PS-UCNPs bind to the digoxigenin end of the cPCR amplicons. Finally, the streptavidin labelled magnetic beads were used to selectively capture the PS-UCNP-labelled cPCR amplicons and the upconversion signal was detected at 537nm under 980nm excitation. This sandwich approach enables direct recognition of the target lambda DNA with a detection limit of 103 copies μL-1. The upconversion signal decreased proportionally to the concentration of the lambda DNA with a linear response between 107 and 103 copies of DNA. Graphical abstract Schematic representation of polystyrene-encapsulated upconversion nanoparticles (PS-UCNPs) prepared by mini-emulsion polymerisation. The PS-UCNPs were functionalised with anti-digoxigenin antibody using the fusion protein linker-protein G (LPG). Detection of digoxigenin-labelled amplicons is achieved (a) by using the antibody-functionalised LPG@PS-UCNP labels; (b) magnetic separation, and (c) 980nm laser light for detection of the green upconversion luminescence peaking at 537nm.

DNA Authentication of St John’s Wort (Hypericum perforatum L.) Commercial Products Targeting the ITS Region

There is considerable potential for the use of DNA barcoding methods to authenticate raw medicinal plant materials, but their application to testing commercial products has been controversial. A simple PCR test targeting species-specific sequences within the nuclear ribosomal internal transcribed spacer (ITS) region was adapted to screen commercial products for the presence of Hypericum perforatum L. material. DNA differing widely in amount and extent of fragmentation was detected in a number of product types. Two assays were designed to further analyse this DNA using a curated database of selected Hypericum ITS sequences: A qPCR assay based on a species-specific primer pair spanning the ITS1 and ITS2 regions, using synthetic DNA reference standards for DNA quantitation and a Next Generation Sequencing (NGS) assay separately targeting the ITS1 and ITS2 regions. The ability of the assays to detect H. perforatum DNA sequences in processed medicines was investigated. Out of twenty different matrices tested, both assays detected H. perforatum DNA in five samples with more than 103 ITS copies µL−1 DNA extract, whilst the qPCR assay was also able to detect lower levels of DNA in two further samples. The NGS assay confirmed that H. perforatum was the major species in all five positive samples, though trace contaminants were also detected.

Exponential rolling circle amplification coupled with lateral flow dipstick strips as a rapid and sensitive method for the field detection of Karlodinium veneficum

Harmful algal blooms (HABs) caused by microalgae pose a great threat to human health, marine ecosystems, tourism, and aquaculture worldwide. Efficient, sensitive, and simple methods for the detection of harmful microalgal species must be developed to reduce the economic losses and damages caused by HABs. This study successfully established a novel method for the detection of the globally distributed HAB-forming species Karlodinium veneficum. The developed method was based on exponential rolling circle amplification (E-RCA) coupled with lateral flow dipstick (LFD) strips. A special oligonucleotide sequence-padlock probe (PLP) was designed on basis of the molecular cloning and subsequent sequencing of the D1–D2 region of the large subunit ribosomal DNA (LSU rDNA) of K. veneficum. The E-RCA reaction system was then established. E-RCA products could be visually analyzed through 2% agarose gel electrophoresis and the LFD assay. The optimized E-RCA conditions were as follows: PLP concentration of 20 pM, ligation cycle number of 12, ligation temperature of 56 °C, amplification duration of 45 min, and amplification temperature of 61 °C. The developed E-RCA-LFD assay was specific for K. veneficum and did not display cross-reactivity with other microalgal species. The E-RCA-LFD assay was 100-fold more sensitive than conventional polymerase chain reaction (PCR) and had detection limits of 8.0 × 101 ag μL−1 for the genomic DNA of K. veneficum and 5.0 × 101 ag μL−1 (approximately 13 copies μL−1) for recombinant plasmids containing the LSU rDNA D1–D2 regions of K. veneficum. Simulative tests indicated that the E-RCA-LFD assay demonstrated considerably higher sensitivity than conventional PCR and a detection limit of 0.01 cell mL−1. The practicability of the E-RCA-LFD assay was confirmed through tests with field samples. In conclusion, the highly sensitive, specific, and facile E-RCA-LFD assay established in this work may enable the field monitoring of natural samples containing K. veneficum.

Droplet Volume Variability and Impact on Digital PCR Copy Number Concentration Measurements.

Digital polymerase chain reaction (dPCR) is increasingly being adopted by reference material producers and metrology institutes for value assignment, and for homogeneity and stability studies of nucleic acid reference materials. A reference method procedure should fulfill several requirements, and the uncertainty and biases should be completely understood. A bias in target concentration when inaccurate droplet volume is used in the droplet dPCR measurement equation has previously been documented. In this study, we characterize both intrawell and interwell droplet volume variability using optical microscopy and determine the impact of these two sources of variability on target concentration estimates. A small optical distortion across the image was measured which, without correction, biased droplet volume measurements. Longitudinal monitoring of interwell droplet volume over 39 weeks using several lots of Mastermix demonstrated a mean droplet volume of 0.786 nL and intermediate precision of 1.7%. The frequency distribution of intrawell droplet volumes varied. Some wells displayed a skewed distribution which resulted in a small bias in estimated target concentration for a simulated dPCR with target concentrations of between 62 and 8000 copies μL-1. The size and direction of this bias was influenced by the distribution pattern of the droplet volumes within the well. The proportion of Mastermix in dPCR mix affected droplet volume. A pipetting error of 10% during mixing of the premix and Mastermix resulted in a 2.6% change in droplet volume and, consequently, a bias in concentration measurements highlighting the advantages of gravimetric preparation of dPCR mixes for high accuracy measurements.