Lower cost alternatives for molecular diagnosis of COVID-19: conventional RT-PCR and SYBR Green-based RT-qPCR.

In March 2020, WHO declared a pandemic state due to SARS-CoV-2 having spread. TaqMan-based real-time RT-qPCR is currently the gold standard for COVID-19 diagnosis. However, it is a high-cost assay, inaccessible for the majority of laboratories around the world, making it difficult to diagnose on a large scale. The objective of this study was to standardize lower cost molecular methods for SARS-CoV-2 identification. E gene primers previously determined for TaqMan assays by Colman et al. (2020) were adapted in SYBR Green assay and RT-PCR conventional. The cross-reactivity test was performed with 17 positive samples for other respiratory viruses, and the sensibility test was performed with 8 dilutions (10 based) of SARS-CoV-2 isolated and 63 SARS-CoV-2-positive samples. The SYBR Green assays and conventional RT-PCR have not shown amplification of the 17 respiratory samples positives for other viruses. The SYBR Green-based assay was able to detect all 8 dilutions of the isolate. The conventional PCR detected until 107 dilution, both assays detected the majority of the 63 samples, 98.42% of positivity in SYBR Green, and 93% in conventional PCR. The average Ct variation between SYBR Green and TaqMan was 1.92 and the highest Ct detected by conventional PCR was 35.98. Both of the proposed assays are less sensitive than the current gold standard; however, our data shows a low sensibility variation, suggesting that these methods could be used by laboratories as a lower cost molecular method for SARS-CoV-2 diagnosis.

Simple and Cost-effective "Turn-on" Fluorescence Sensor for the Determination of Xanthine.

A simple and selective 'turn-on' fluorescence sensor have been developed for the determination of xanthine (XA) based on glutathione (GSH) capped copper nanoclusters (CuNCs) as the fluorescent probe. The proposed sensor possess several advantages such as sensitivity, short analysis time and requires no sample pretreatment. The conditions for the performances of the sensor have been optimized and good linear relationship was obtained between concentration and relative fluorescence intensity in the concentration range 9.0[Formula: see text]10-3 M to 8.0[Formula: see text]10-5 M with a detection limit 6.0[Formula: see text]10-6 M. The mechanism behind the fluorescence enhancement may be ascribed to the binding of XA on the surface of GSH CuNCs. The sensor have been successfully applied to determine XA in spiked physiological samples.

Activatable fluorescent probes in fluorescence-guided surgery: Practical considerations.

Fluorescence-guided imaging during surgery is a promising technique that is increasingly used to aid surgeons in identifying sites of tumor and surgical margins. Of the two types of fluorescent probes, always-on and activatable, activatable probes are preferred because they produce higher target-to-background ratios, thus improving sensitivity compared with always-on probes that must contend with considerable background signal. There are two types of activatable probes: 1) enzyme-reactive probes that are normally quenched but can be activated after cleavage by cancer-specific enzymes (activity-based probes) and 2) molecular-binding probes which use cancer targeting moieties such as monoclonal antibodies to target receptors found in abundance on cancers and are activated after internalization and lysosomal processing (binding-based probes). For fluorescence-guided intraoperative surgery, enzyme-reactive probes are superior because they can react quickly, require smaller dosages especially for topical applications, have limited side effects, and have favorable pharmacokinetics. Enzyme-reactive probes are easier to use, fit better into existing work flows in the operating room and have minimal toxicity. Although difficult to prove, it is assumed that the guidance provided to surgeons by these probes results in more effective surgeries with better outcomes for patients. In this review, we compare these two types of activatable fluorescent probes for their ease of use and efficacy.

A simple and cost effective method for preparing FL and LG solutions.

PURPOSE: The purpose of this study was to develop a clinically feasible method for obtaining dye concentrations of 2% fluorescein (FL) and 1% lissamine green (LG) by soaking commercially available dye impregnated strips in saline. METHODS: Calibration curves were established to related known concentrations of dye to prepared FL fluorescence and LG absorbance. To determine the optimum number of dye strips and soaking times (preliminary testing), 1, 2, 3 FL or LG strips were soaked in 200 µl commercially available saline for 0.5, 1, 2, 3, 4 and 5 min, using calibration curves to determine FL and LG concentrations. The best combination of number of dye strips and soaking time was soaking 3FL and 3LG strips for 5 min and these were finally tested in 2 ml centrifuge tubes, selected for ease of use in a clinical setting. RESULTS: Preliminary testing indicated that soaking 3 FL or 3 LG strips for 5 min in saline yielded an average (±standard deviation) of 2.0 ± 0.000% FL and 0.93 ± 0.010% LG. Final testing of FL in centrifuge tubes (strips soaked for 3-15 min) yielded an average of 1.99 ± 0.040% FL, with no significant difference among time periods or dye lots tested. However, LG showed more variable results with an average of 0.80 ± 0.160% LG (5-15 min), with significant differences among dye lots and times (2-way ANOVA, p < 0.05). CONCLUSIONS: This simple, reliable and relatively inexpensive method involves soaking 3 FL or LG strips in saline solution, yielding concentrations close to the 2%FL and 1%LG recommended for clinical trials, although LG showed more variability.

Indocyanine Green Angiography Use in Breast Reconstruction: A National Analysis of Outcomes and Cost in 110,320 Patients.

BACKGROUND: Indocyanine green angiography has gained popularity in breast reconstruction for its ability to assess mastectomy skin and tissue flap viability. The authors aim to analyze trends and outcomes associated with indocyanine green angiography use in breast reconstruction. METHODS: Using 2012 to 2014 data from the Healthcare Cost and Utilization Project National Inpatient Sample, Agency for Healthcare Research and Quality, the authors identified breast reconstructions performed with or without indocyanine green angiography use. Trends over time were assessed using the Cochran-Armitage test. Outcomes were assessed using logistic regression and generalized linear modeling. RESULTS: Over the study period, 110,320 patients underwent breast reconstruction: 107,005 (97.0 percent) without and 3315 (3.0 percent) with indocyanine green angiography use. Usage increased over time: 750 patients (1.9 percent) in 2012, increasing to 1275 patients (3.7 percent) in 2013 (p < 0.001). Smokers (p = 0.018), hypertensive patients (p = 0.046), obese patients (p < 0.001), and those with a higher comorbidity index (p < 0.001) were more likely to undergo indocyanine green angiography. Autologous reconstruction was more frequently combined with its use compared with tissue expander reconstruction (4.5 percent versus 2.1 percent; p < 0.001). There was a significant increase in the odds of débridement associated with its use (OR, 1.404; p < 0.001; 95 percent CI, 1.201 to 1.640). CONCLUSIONS: Indocyanine green angiography use in breast reconstruction has increased in recent years and is associated with higher débridement rates. These rates may indicate changing trends for clinicians when deciding whether to débride tissue during breast reconstruction. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, III.

Reconsidering the H&E stain as the gold standard in assessing the depth of burn wounds.

While histological examination is considered by most as the gold standard for burn depth assessment, it has no practical use in the clinical setting. It has, however, been used in the research setting, as a mean for evaluating emerging techniques of depth measurement. Due to the limitations of the H&E stain, other stains have also been explored, such as lactate dehydrogenase (LDH), as presented in this issue, in "Improving the Histologic Characterization of Burn Depth." As the determination of burn depth is not a typical subject in dermatopathology, a summary of selected techniques and the possible role for the LDH stain in future research, is described herein.

Cost-effectiveness of Early Division of the Forehead Flap Pedicle.

IMPORTANCE: The paramedian forehead flap is considered the gold standard procedure to optimally reconstruct major defects of the nose, but this procedure generally requires 2 stages, where the flap pedicle is divided 3 weeks following the initial surgery to ensure adequate revascularization of the flap from the surrounding recipient tissue bed, which can cost a patient time out of work or away from normal social habits. It has previously been shown that the pedicle may be safely divided after 2 weeks in select patients where revascularization from the recipient bed was confirmed using intraoperative laser fluorescence angiography to potentially save the patient time and money. OBJECTIVE: To demonstrate the cost-effectiveness of takedown of the paramedian forehead flap pedicle after 2 weeks using angiography with indocyanine green (ICG). DESIGN, SETTING, AND PARTICIPANTS: Retrospective cohort study of all patients who underwent 2-week division of the forehead flap after nasal reconstruction. Patient, tumor, defect, and outcomes data were collected. Cost-minimization analysis was performed by comparing the overall costs of 2-week takedown with angiography to a hypothetical patient undergoing 3-week takedown without angiography. INTERVENTION: Two-week division of the forehead flap after nasal reconstruction. MAIN OUTCOMES AND MEASURES: Cost-minimization analysis performed by calculating the total variable costs for a patient in our cohort vs costs to a theoretical patient for whom angiography was not performed and the pedicle was divided at the 3-week mark. RESULTS: A total of 22 patients were included (mean [SD] age, 70.3 [10.0] years; 8 women [36.4%] and 14 men [63.6%]). The selection criteria for 2-week division of the pedicle are a wound bed with at least 50% vascularized tissue present, partial-thickness defects, and absence of nicotine use. All were divided at the 2-week mark with no instances of flap necrosis. One patient had a squamous eccrine carcinoma histology before reconstruction, all other patients had basal cell carcinoma, squamous cell carcinoma, and melanoma. Cost-minimization analysis showed that the use of angiography with ICG results in cost savings of $177 per patient on average. CONCLUSIONS AND RELEVANCE: Two-week takedown of select paramedian forehead flap patients can be performed safely with verification using angiography with ICG. Although this technology inherently adds cost, it is cost-effective, saving a total of $177 per patient. LEVEL OF EVIDENCE: NA.

Sensitive detection of proteins in polyacrylamide gel via isatoic anhydride derivatization: Introduction of a low-cost fluorescent prelabeling procedure.

Here, we introduce isatoic anhydride as a sensitive and commodious fluorescent prelabel for detection of proteins in one-dimensional polyacrylamide gels. High reactivity of isatoic anhydride with nucleophiles in mild alkaline environments makes it an appropriate tag for labeling of biomolecules. In this study, we show that preelectrophoresis labeling of proteins with isatoic anhydride for few minutes at room temperature allows detection of 2-4 ng of standard proteins, BSA and lysozyme, per band. Proteins were successfully labeled in the presence of a wide range of common biological reagents and in crude cell extract. The labeled proteins have the same electrophoretic migration in comparison to unlabeled proteins; however the application of saturation labeling method results in slight band broadening. Compatibility of the method with downstream processes was assessed by tryptic digestion of labeled proteins and study of peptide mixture using gel electrophoresis which revealed partial digestion of labeled proteins due to lysine modification. The present procedure is sensitive, rapid, and inexpensive and is a promising alternative for current protein staining procedures, where downstream processes are not desired.

Terbium fluorescence as a sensitive, inexpensive probe for UV-induced damage in nucleic acids.

Much effort has been focused on developing methods for detecting damaged nucleic acids. However, almost all of the proposed methods consist of multi-step procedures, are limited, require expensive instruments, or suffer from a high level of interferences. In this paper, we present a novel simple, inexpensive, mix-and-read assay that is generally applicable to nucleic acid damage and uses the enhanced luminescence due to energy transfer from nucleic acids to terbium(III) (Tb(3+)). Single-stranded oligonucleotides greatly enhance the Tb(3+) emission, but duplex DNA does not. With the use of a DNA hairpin probe complementary to the oligonucleotide of interest, the Tb(3+)/hairpin probe is applied to detect ultraviolet (UV)-induced DNA damage. The hairpin probe hybridizes only with the undamaged DNA. However, the damaged DNA remains single-stranded and enhances the intrinsic fluorescence of Tb(3+), producing a detectable signal directly proportional to the amount of DNA damage. This allows the Tb(3+)/hairpin probe to be used for sensitive quantification of UV-induced DNA damage. The Tb(3+)/hairpin probe showed superior selectivity to DNA damage compared to conventional molecular beacons probes (MBs) and its sensitivity is more than 2.5 times higher than MBs with a limit of detection of 4.36±1.2 nM. In addition, this probe is easier to synthesize and more than eight times cheaper than MBs, which makes its use recommended for high-throughput, quantitative analysis of DNA damage.

Efficient solid phase strategy for preparation of modified xanthene dyes for biolabelling.

An efficient solid phase strategy for the versatile functionalisation of xanthene dyes for conjugation and labelling of biomolecules is presented. The low cost, high purity and excellent spectral properties of the obtained materials provide an attractive alternative for the labelling of a wide range of molecules.

Real-time quantitative PCR with SYBR Green I detection for estimating copy numbers of nine drug resistance candidate genes in Plasmodium falciparum.

BACKGROUND: Evaluating copy numbers of given genes in Plasmodium falciparum parasites is of major importance for laboratory-based studies or epidemiological surveys. For instance, pfmdr1 gene amplification has been associated with resistance to quinine derivatives and several genes involved in anti-oxidant defence may play an important role in resistance to antimalarial drugs, although their potential involvement has been overlooked. METHODS: The DeltaDeltaCt method of relative quantification using real-time quantitative PCR with SYBR Green I detection was adapted and optimized to estimate copy numbers of three genes previously indicated as putative candidates of resistance to quinolines and artemisinin derivatives: pfmdr1, pfatp6 (SERCA) and pftctp, and in six further genes involved in oxidative stress responses. RESULTS: Using carefully designed specific RT-qPCR oligonucleotides, the methods were optimized for each gene and validated by the accurate measure of previously known number of copies of the pfmdr1 gene in the laboratory reference strains P. falciparum 3D7 and Dd2. Subsequently, Standard Operating Procedures (SOPs) were developed to the remaining genes under study and successfully applied to DNA obtained from dried filter blood spots of field isolates of P. falciparum collected in São Tomé & Principe, West Africa. CONCLUSION: The SOPs reported here may be used as a high throughput tool to investigate the role of these drug resistance gene candidates in laboratory studies or large scale epidemiological surveys.

Comparative analysis of the DNA staining efficiencies of different fluorescent dyes in preparative agarose gel electrophoresis.

Ethidium bromide (EB) is a mutagen and toxin that is widely used in the laboratory for visualization of nucleic acids. Safer nucleic acid stains, such as SYBR Gold, SYBR Green, GoldView, GeneFinder, and GoldStar, have been developed. However, there has been no systematic comparative analysis of the staining efficiencies of these dyes. In the present study, SYBR Gold, SYBR Green I, GoldView and EB were compared. Although both SYBR Gold and SYBR Green alter electrophoretic mobility and thus DNA size estimates, they are cost-effective alternatives to EB. SYBR Gold was more sensitive than SYBR Green I at detecting short fragments, but 50-bp bands were clearly visible using either dye when visualized with a long integration time. SYBR Gold or SYBR Green I are sensitive and relatively safe alternatives to EB. In our laboratory, the SYBR Gold method is now used routinely by all members of our group with great consistency and success.

In vitro drug interactions of cytochrome p450: an evaluation of fluorogenic to conventional substrates.

Clinically observed drug interactions with cytochrome p450 (p450) enzymes have increased the need to assess drug interactions of new chemical entities early in the discovery process. To meet this need, fluorogenic substrates have been commercialized. However, only limited evaluations of their utility and comparisons to drug probes have been reported. This study examines the correlation between IC50 values obtained with fluorogenic and conventional drug probes for structurally diverse inhibitors of the five major human p450 isoforms. In general, correlations are weak, with significant numbers of compounds being missed as inhibitors by either probe. For p450s 1A2, 2C9, and 2C19, correlation coefficients were above 0.6 with slopes that ranged from 1.5 to 4.2. However, for p450s 1A2 and 2C9, about 20% of compounds were not included because an IC50 value could not be determined with one of the two probes. CYP 2C19 had the highest correlation (correlation coefficient 0.84), with a slope of 2.0 and less than 5% of compounds excluded. CYP 2D6 showed a good correlation for IC50 values less than 10 microM. However, at higher IC50 values, a high degree of scatter was observed. CYP 3A4 had the weakest correlation, and a large number of compounds were excluded with the fluorogenic probe. Overall, the study shows the care needed when selecting fluorogenic probes and the caution needed when results with fluorogenic probes are used to drive structure-activity relationships with respect to drug interactions.

Quantitative assessment of the importance of dye switching and biological replication in cDNA microarray studies.

Dye switching and biological replication substantially increase the cost and the complexity of cDNA microarray studies. The objective of the present analysis was to quantitatively assess the importance of these procedures to provide a quantitative basis for decision-making in the design of microarray experiments. Taking advantage of the unique characteristics of a published data set, the impact of these procedures on the reliability of microarray results was calculated. Adding a second microarray with dye switching substantially increased the correlation coefficient between observed and predicted ln(ratio) values from 0.38 +/- 0.06 to 0.62 +/- 0.04 (n = 12) and the outlier concordance from 21 +/- 3% to 43 +/- 4%. It also increased the correlation with the entire set of microarrays from 0.60 +/- 0.04 to 0.79 +/- 0.04 and the outlier concordance from 31 +/- 6% to 58 +/- 5% and tended to improve the correlation with Northern blot results. Adding a second microarray to include biological replication also improved the performance of these indices but often to a lesser degree. Inclusion of both procedures in the second microarray substantially improved the consistency with the entire set of microarrays but had minimal effect on the consistency with predicted results. Analysis of another data set generated using a different cDNA labeling method also supported a significant impact of dye switching. In conclusion, both dye switching and biological replication substantially increased the reliability of microarray results, with dye switching likely having even greater benefits. Recommendations regarding the use of these procedures were proposed.

Ultrasensitive detection of genetically modified maize DNA by capillary gel electrophoresis with laser-induced fluorescence using different fluorescent intercalating dyes.

In this work, four different fluorescent intercalating dyes are compared for the ultrasensitive CGE-LIF detection of DNA from transgenic maize in flours. The fluorescent intercalating dyes compared are YOPRO-1, SYBR-Green-I, Ethidium bromide (EthBr), and EnhanCE. For all the four dyes optimum concentrations are established, and efficient separations of DNA fragments ranging in size from 80 to 1000 bp are obtained. The comparative study demonstrates that SYBR-Green-I and YOPRO-1 provide better limits of detection (LODs) than EnhanCE or EthBr (i.e., LODs are, respectively, 700, 1000, 11300, and 97400 zmol, calculated for a 200-bp DNA fragment). Separations using YOPRO-1 are faster than those using SYBR-Green-I (30 min vs 47 min for the analysis of the 80-1000 bp DNA fragments). Also, separations using YOPRO-1 are more efficient than those using SYBR-Green-I (e.g., 2.4 x 10(6) plates/m vs 1.6 x 10(6) plates/m, respectively, calculated for the 200-bp fragment). Also, buffer depletion and cost per analysis are worse with SYBR-Green-I than with YOPRO-1. Therefore, YOPRO-1 was selected as the preferred intercalating dye. Using this fluorescent compound, analysis time reproducibility for the CGE-LIF separation of the DNA fragments is determined to be better than 1.7% (% RSD, n = 10) within the same day, and better than 1.9% (% RSD, n = 30) for three different days. Moreover, the fluorescence signal obtained using this dye is shown to vary linearly with the DNA concentration in the range studied, i.e., 1-500 ng/microL. It is demonstrated that by using this method 0.01% of transgenic maize can be detected in flour by direct injection of the PCR-amplified sample.

Microquantification of cellular and in vitro F-actin by rhodamine phalloidin fluorescence enhancement.

Based on the enhancement of rhodamine phalloidin fluorescence after its binding to actin filaments we have developed a technique to quantify F-actin, drastically (>> 100 times) reducing consumption of the expensive fluorescent dye and sample material in comparison to previous methods. Depolymerization of F-actin is prevented by utilizing short incubation times and stabilization of the filaments by actin-binding proteins or formaldehyde. Equilibrium and kinetic mathematical models relating rhodamine fluorescence with F-actin concentrations were used to predict the optimal assay conditions. The method has been applied to measure relative and absolute F-actin concentrations in cytosolic fractions and stimulus-induced actin polymerization in neutrophils. The cells were lysed with octy1-beta-D-glucopyranoside, which is compatible with the assay due to its high critical micelle concentration. As the assay takes less than 1 h and eliminates all previously required washing or extraction steps, it is faster and much simpler than any other presented up to now for quantification of filamentous actin. Moreover, the method is unique for reliable and easy F-actin measurements in cell-free systems.