Nonspecific Fluorescence Research Articles

Dual-Locked Enzyme-Activatable Bioorthogonal Fluorescence Turn-On Imaging of Senescent Cancer Cells.

Bioorthogonal pretargeting optical imaging shows the potential for enhanced diagnosis and prognosis. However, the bioorthogonal handles, known for being "always reactive", may engage in reactions at unintended sites with their counterparts, resulting in nonspecific fluorescence activation and diminishing detection specificity. Meanwhile, despite the importance of detecting senescent cancer cells in cancer therapy, current methods mainly rely on common single senescence-associated biomarkers, which lack specificity for differentiating between various types of senescent cells. Herein, we report a dual-locked enzyme-activatable bioorthogonal fluorescence (DEBOF) turn-on imaging approach for the specific detection of senescent cancer cells. A dual-locked bioorthogonal targeting agent (DBTA) and a bioorthogonally activatable fluorescent imaging probe (BAP) are synthesized as the biorthogonal pair. DBTA is a tetrazine derivative dually caged by two enzyme-cleavable moieties, respectively, associated with senescence and cancer, which ensures that its bioorthogonal reactivity ("clickability") is only triggered in the presence of senescent cancer cells. BAP is a fluorophore caged by trans-cyclooctane (TCO), whose fluorescence is only activated upon bioorthogonal reaction between its TCO and the decaged tetrazine of DBTA. As such, the DEBOF imaging approach differentiates senescent cancer cells from nonsenescent cancer cells or other senescent cells, allowing noninvasive tracking of the population fluctuation of senescent cancer cells in the tumor of living mice to guide cancer therapies. This study thus provides a general molecular strategy for biomarker-activatable in vivo bioorthogonal pretargeting imaging with the potential to be applied to other imaging modalities beyond optics.

Deep learning-based localization algorithms on fluorescence human brain 3D reconstruction: a comparative study using stereology as a reference

3D reconstruction of human brain volumes at high resolution is now possible thanks to advancements in tissue clearing methods and fluorescence microscopy techniques. Analyzing the massive data produced with these approaches requires automatic methods able to perform fast and accurate cell counting and localization. Recent advances in deep learning have enabled the development of various tools for cell segmentation. However, accurate quantification of neurons in the human brain presents specific challenges, such as high pixel intensity variability, autofluorescence, non-specific fluorescence and very large size of data. In this paper, we provide a thorough empirical evaluation of three techniques based on deep learning (StarDist, CellPose and BCFind-v2, an updated version of BCFind) using a recently introduced three-dimensional stereological design as a reference for large-scale insights. As a representative problem in human brain analysis, we focus on a 4-cm3\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$4~\ ext {-cm}^3$$\\end{document} portion of the Broca’s area. We aim at helping users in selecting appropriate techniques depending on their research objectives. To this end, we compare methods along various dimensions of analysis, including correctness of the predicted density and localization, computational efficiency, and human annotation effort. Our results suggest that deep learning approaches are very effective, have a high throughput providing each cell 3D location, and obtain results comparable to the estimates of the adopted stereological design.

A Point-of-Care Nucleic Acid Quantification Method by Counting Light Spots Formed by LAMP Amplicons on a Paper Membrane.

Nucleic acid quantification, allowing us to accurately know the copy number of target nucleic acids, is significant for diagnosis, food safety, agricultural production, and environmental protection. However, current digital quantification methods require expensive instruments or complicated microfluidic chips, making it difficult to popularize in the point-of-care detection. Paper is an inexpensive and readily available material. In this study, we propose a simple and cost-effective paper membrane-based digital loop-mediated isothermal amplification (LAMP) method for nucleic acid quantification. In the presence of DNA fluorescence dyes, the high background signals will cover up the amplicons-formed bright spots. To reduce the background fluorescence signals, a quencher-fluorophore duplex was introduced in LAMP primers to replace non-specific fluorescence dyes. After that, the amplicons-formed spots on the paper membrane can be observed; thus, the target DNA can be quantified by counting the spots. Take Vibrio parahaemolyticus DNA detection as an instance, a good linear relationship is obtained between the light spots and the copy numbers of DNA. The paper membrane-based digital LAMP detection can detect 100 copies target DNA per reaction within 30 min. Overall, the proposed nucleic acid quantification method has the advantages of a simple workflow, short sample-in and answer-out time, low cost, and high signal-to-noise, which is promising for application in resourced limited areas.

A FACS-based novel isolation technique identifies heterogeneous CTCs in oral squamous cell carcinoma.

Isolating circulating tumour cells (CTCs) from the blood is challenging due to their low abundance and heterogeneity. Limitations of conventional CTC detection methods highlight the need for improved strategies to detect and isolate CTCs. Currently, the Food and Drug Administration (FDA)-approved CellSearch™ and other RUO techniques are not available in India. Therefore, we wanted to develop a flexible CTC detection/isolation technique that addresses the limitation(s) of currently available techniques and is suitable for various downstream applications. We developed a novel, efficient, user-friendly CTC isolation strategy combining density gradient centrifugation and immuno-magnetic hematogenous cell depletion with fluorescence-activated cell sorting (FACS)-based positive selection using multiple CTC-specific cell-surface markers. For FACS, a stringent gating strategy was optimised to exclude debris and doublets by side scatter/forward scatter (SSC/FSC) discriminator, remove dead cells by 4',6-diamidino-2-phenylindole (DAPI) staining, and eliminate non-specific fluorescence using a "dump" channel. APC-labelled anti-CD45mAB was used to gate remaining hematogenous cells, while multiple epithelial markers (EpCAM, EGFR, and Pan-Cytokeratin) and an epithelial-mesenchymal transition (EMT) marker (Vimentin) labelled with fluorescein isothiocyanate (FITC) were used to sort cancer cells. The technique was initially developed by spiking Cal 27 cancer cells into the blood of healthy donors and then validated in 95 biopsy-proven oral squamous cell carcinoma (OSCC) patients. CTCs isolated from patients were reconfirmed by Giemsa staining, immuno-staining, and whole transcriptome amplification (WTA), followed by qRT-PCR. In vitro culture and RNA sequencing (RNA-Seq) were also performed to confirm their suitability for various downstream applications. The mean detection efficiency for the Cal 27 tongue cancer cells spiked in the whole blood of healthy donors was 32.82% ± 12.71%. While ~75% of our patients (71/95) had detectable CTCs, the CTC positivity was independent of the TNM staging. The isolated potential cancer cells from OSCC patients were heterogeneous in size. They expressed different CTC-specific markers in various combinations as identified by qRT-PCR after WTA in different patients. Isolated CTCs were also found to be suitable for downstream applications like short-term CTC culture and RNA-Seq. We developed a sensitive, specific, flexible, and affordable CTC detection/isolation technique, which is scalable to larger patient cohorts, provides a snapshot of CTC heterogeneity, isolates live CTCs ready for downstream molecular analysis, and, most importantly, is suitable for developing countries.

CRISPR-Cas14a with competitive isothermal amplification for rapid visual pathogen diagnosis

The aquatic foodborne pathogen-induced infectious disease is becoming one of the killers to people’s health worldwide, attributed to its long latent period and high infectivity. It is urgently desiderated to develop simple, rapid, sensitive and universal detection techniques for early diagnosis and timely treatment of pathogens. Here, we present a novel visible CRISPR biosensing pathogen detection system named integrating competitive annealing mediated isothermal amplification (CAMP) -mediated CRISPR-Cas14a isothermal detection platform (CCIP) through CAMP with CRISPR-Cas14a. Initially, in the presence of target gene, CAMP was conducted at constant temperature to produce folded CAMP amplicon with abundant single-stranded DNA (ssDNA) target sites. When Cas14a-small guide RNA (sgRNA) binary complex specially recognized target sequences, it would trigger the cleavage collateral activity on nonspecific ssDNA fluorescence probes to produce optical signal with a quite high turnover. Furthermore, the results could be easily observed by naked eyes in an hour with high specificity and sensitivity of 102 aM. Furthermore, the method was verified with a pathogen detection result of 100% accuracy for 15 whole blood samples. Thus, CCIP is a promising point-of-care testing (POCT) technique for practical pathogen diagnosis.

A novel method for the whole-cell detection of environmental microorganisms using hemin and tyramide signal amplification (Hemin-TSA) with a desired fluorescent dye

A method called hemin-tyramide signal amplification (Hemin-TSA) was developed for visualization of environmental microorganisms using hemin and tyramide signal amplification. In Hemin-TSA, hemin, which has peroxidase activity, is bound to microbial cells, and a desired fluorescent dye is deposited on the microbial cells by a hemin-catalyzed TSA reaction. The protocol was initially optimized in terms of hemin concentration, hemin binding time and repeated reaction times of TSA. Hemin-TSA showed a comparative or improved signal-to-noise ratio compared to DAPI staining. The shapes of fluorescent signals obtained from microbial cells were almost morphologically identical to those observed in phase contrast microscopy. Hemin-TSA staining provided more accurate cell counts than DAPI staining, especially for actively growing cells, for which two or three spotty DAPI signals were obtained from a single cell. In addition, microbial cells that were not detected by DAPI staining were detected by Hemin-TSA with fluorescein, which enabled us to avoid high non-specific fluorescence under UV excitation. The method developed in this study allows us to visually detect microbial cells in various environments with the characteristics of better cell morphological identification, improved enumeration accuracy and selectivity of fluorescent dyes.

The World's First Acne Dysbiosis-like Model of Human 3D Ex Vivo Sebaceous Gland Colonized with Cutibacterium acnes and Staphylococcus epidermidis.

Acne-prone skin is associated with dysbiosis involving Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) causing increased seborrhea in sebaceous glands (SG) and inflammation. Human primary sebocytes were cultivated using 1.106 UFC/mL C. acnes Type IA (facial acne, ATCC6919) and/or 1.105 UFC/mL S. epidermidis (unknown origin, ATCC12228) for 48 h in our SEB4GLN-optimized media without antibiotics. Bacteria and sebocytes were enumerated and assessed to determine their viability. Lipid production was imaged and quantified via Nile Red staining. SG with hair follicles were microdissected from healthy skin and cultured using 1.105 UFC/mL C. acnes Type 1A and/or 1.104 UFC/mL S. epidermidis (wild-type facial skin strain) through prior fixation and immunostaining for MC5R, C. acnes and nuclei (DAPI) via Z-stack confocal microscopy bioimaging (Leica SP5X & FIJI software, Version 2.9.0). C. acnes growth was not impacted when co-cultivated with sebocytes (2D) or SG (3D) models. Phylotype IA stimulated sebocyte lipid production, which had no impact on viability. The S. epidermidis reference strain overproliferated, inducing sebocyte mortality. For 3D SG model, culture conditions were optimized using a wild-type facial skin strain at a lower concentration, 1:10 ratio to C. acnes, reduced contact time, sequential inoculation and rinsing step. Bioimaging revealed strong C. acnes labeling in the active areas of the pilosebaceous unit. S. epidermidis formed biofilm, which was distributed across the SG via non-specific fluorescence imaging. We developed an innovative model of a sebaceous gland that mimics acne-prone skin with lipid overproduction and virulent phylotype IA C. acnes inoculation.

Establishment of an indirect immunofluorescence assay for the detection of African swine fever virus antibodies

African swine fever (ASF) continues to cause enormous economic loss to the global pig industry. Since there is no safe and effective vaccine, accurate and timely diagnosis of ASF is essential to implement control measures. Indirect immunofluorescence assay (IFA) is a gold standard serological method recommended by the World Organization for Animal Health (WOAH). In this study, we used primary fetal kidney cells to establish a wild boar cell line (BK2258) that supported the efficient replication of ASF virus (ASFV) SD/DY-I/21 and showed visible cytopathic effect (CPE). Moreover, using BK2258, we established a sensitive and specific IFA for ASFV antibody detection. To standardize and evaluate the performance of this assay, we used serum samples from pigs infected with the low virulent genotype I SD/DY-I/21 and genotype II HLJ/HRB1/20, and immunized with the vaccine candidate HLJ/18-7GD, field samples, and negative serum samples. The IFA reacted with the ASFV-positive sera and displayed bright fluorescence foci. There was no non-specific green fluorescence due to cellular senescence or other cell damage-causing factors. Compared to a commercial indirect enzyme-linked immunosorbent assay (iELISA), ASFV antibodies were detected 1–4 days earlier using our IFA. The detection limits of the IFA and iELISA for the same ASFV-antibody positive serum samples were 1:25,600 and 1:6,400, respectively, indicating that the IFA is more sensitive than iELISA. The newly established IFA was highly specific and did not cross-react with sera positive for six other important porcine pathogens (i.e., Classical swine fever virus (CSFV), Porcine reproductive and respiratory syndrome virus (PRRSV), Porcme circovirus type 2 (PCV2), Pseudorabies virus (PRV), Foot-and-Mouth disease virus type O (FMDV/O), and Porcine epidemic diarrhea virus (PEDV)). This study thus provides a sensitive, specific, and reliable detection method that is suitable for the serological diagnosis of ASF.

A Highly Selective Mn(II)-Specific DNAzyme and Its Application in Intracellular Sensing.

Manganese is an essential trace element in the human body that acts as a cofactor in many enzymes and metabolisms. It is important to develop methods to detect Mn2+ in living cells. While fluorescent sensors have been very effective in detecting other metal ions, Mn2+-specific fluorescent sensors are rarely reported due to nonspecific fluorescence quenching by the paramagnetism of Mn2+ and poor selectivity against other metal ions such as Ca2+ and Mg2+. To address these issues, we herein report in vitro selection of an RNA-cleaving DNAzyme with exceptionally high selectivity for Mn2+. Through converting it into a fluorescent sensor using a catalytic beacon approach, Mn2+ sensing in immune cells and tumor cells has been achieved. The sensor is also used to monitor degradation of manganese-based nanomaterials such as MnOx in tumor cells. Therefore, this work provides an excellent tool to detect Mn2+ in biological systems and monitor the Mn2+-involved immune response and antitumor therapy.

Super-resolution paint imaging with molecular beacon.

DNA-PAINT offers simple super-resolution imaging through the transient binding of fluorescently-labelled DNA imagers to target molecules. It has many advantages, including super-multiplexing capability and robustness against photobleaching. However, the unbound fluorescent imagers in the solution can cause high fluorescence background and place constraints on the imaging conditions that limit the technique's potential, such as low imager concentration, thin TIRF illumination, and long exposure time. In this study, we developed a new strategy to improve PAINT imaging using a fluorogenic molecular beacon (MB) as the imager. MB-PAINT eliminates false localizations from nonspecific surface adsorption and fluorescence background at concentrations far exceeding conventional linear imagers. Furthermore, MB-PAINT achieves similar nanometer localization precision to conventional DNA-PAINT. Lastly, we demonstrate that MB-PAINT is ideally suited for super-resolution tension imaging in living cells even at high frame rates, suppressing the potential of artifacts from free-diffusing and spontaneous binding of imagers at the cell-substrate interface.

Hybrid Micelles of Carbon Quantum Dot-Doxorubicin Conjugates as Nanotheranostics for Tumor Therapy and Turn-On Fluorescence Imaging: Impact of Conjugated Structures and On-Off-On Mechanism.

Carbon quantum dots (CDs) have attracted more and more attention in the field of biological imaging, while their applications are restricted due to their nonspecific fluorescence and small particle size. Herein, two pH-responsive carbon quantum dot-doxorubicin (DOX) conjugates were designed with maleic acid (MA, cis-butenedioic acid) and fumaric acid (FA, trans-butenedioic acid) as linker, respectively, which could self-assemble into unique hybrid micelles as tumor-specific carrier-free nanotheranostics. Owing to the acid-labile covalent modification with conjugated groups and the interaction with the surrounding DOX molecules, the fluorescence of CDs was completely quenched, while it could be recovered in the tumor intracellular microenvironment by acid-triggered cleavage of the fluorophore-drug conjugates, showing excellent turn-on fluorescence for effective cellular imaging. Especially, the trans conjugate with FA as linker possessed higher drug content, better drug release behavior and stronger inhibition of tumor cells than the cis one with MA as linker, demonstrating its promising potential as carrier-free nanotheranostics for future tumor treatment.

Intra-operative fluorescence-based detection of positive surgical margins during radical prostatectomy: Lessons learned from a pilot ex vivo translational study.

Nerve-sparing techniques during radical prostatectomy have been associated with an increased risk of positive surgical margins. The intra-operative detection of residual prostatic tissue could help mitigate this risk. The objectives of the present study were to assess the feasibility of using an anti-prostate-specific membrane antigen (anti-PSMA) antibody conjugated with a fluorophore to characterize fresh prostate tissue as prostatic or non-prostatic for intra-operative surgical margin detection. Fresh prostatic tissue samples were collected from transurethral resections of the prostate (TURP) or prostate biopsies, and either immunolabelled with anti-PSMA antibody conjugated with Alexa Fluor 488or used as controls. A dedicated, laparoscopy-compliant fluorescence device was developed for real-time fluorescence detection. Confocal microscopy was used as the gold standard for comparison. Spectral unmixing was used to distinguish specific, Alexa Fluor 488 fluorescence from nonspecific autofluorescence. The average peak wavelength of the immuno-labeled TURP samples (n = 4) was 541.7 ± 0.9 nm and of the control samples (n = 4) was 540.8 ± 2.2 nm. Spectral unmixing revealed that these similar measures were explained by significant autofluorescence, linked to electrocautery. Three biopsy samples were then obtained from seven patients and also displayed significant nonspecific fluorescence, raising questions regarding the reproducibility of the fixation of the anti-PSMA antibodies on the samples. Comparing the fluorescence results with final pathology proved challenging due to the small sample size and tissue alterations. This study showed similar fluorescence of immuno-labeled prostate tissue samples and controls, failing to demonstrate the feasibility of intra-operative margin detection using PSMA immuno-labeling, due to marked tissue autofluorescence. We successfully developed a fluorescence device that could be used intraoperatively in a laparoscopic setting. Use of the infrared rangeas well as newly available antibodies could prove interesting options for future research.

Analytical methods for assessing retinal cell coupling using cut-loading

Electrical coupling between retinal neurons contributes to the functional complexity of visual circuits. "Cut-loading" methods allow simultaneous assessment of cell-coupling between multiple retinal cell-types, but existing analysis methods impede direct comparison with gold standard direct dye injection techniques. In the current study, we both improved an existing method and developed two new approaches to address observed limitations. Each method of analysis was applied to cut-loaded dark-adapted Guinea pig retinae (n = 29) to assess coupling strength in the axonless horizontal cell type ('a-type', aHCs). Method 1 was an improved version of the standard protocol and described the distance of dye-diffusion (space constant). Method 2 adjusted for the geometric path of dye-transfer through cut-loaded cells and extracted the rate of dye-transfer across gap-junctions in terms of the coupling coefficient (kj). Method 3 measured the diffusion coefficient (De) perpendicular to the cut-axis. Dye transfer was measured after one of five diffusion times (1-20 mins), or with a coupling inhibitor, meclofenamic acid (MFA) (50-500μM after 20 mins diffusion). The standard protocol fits an exponential decay function to the fluorescence profile of a specified retina layer but includes non-specific background fluorescence. This was improved by measuring the fluorescence of individual cell soma and excluding from the fit non-horizontal cells located at the cut-edge (p<0.001) (Method 1). The space constant (Method 1) increased with diffusion time (p<0.01), whereas Methods 2 (p = 0.54) and 3 (p = 0.63) produced consistent results across all diffusion times. Adjusting distance by the mean cell-cell spacing within each tissue reduced the incidence of outliers across all three methods. Method 1 was less sensitive to detecting changes induced by MFA than Methods 2 (p<0.01) and 3 (p<0.01). Although the standard protocol was easily improved (Method 1), Methods 2 and 3 proved more sensitive and generalisable; allowing for detailed assessment of the tracer kinetics between different populations of gap-junction linked cell networks and direct comparison to dye-injection techniques.

Optimization of endocrine pancreas fluorescence analysis using machine methods

The study aims to establish the appropriate parameters of UV excitation intensity and permanent excitation time on the pancreatic islets photobleaching, the ratio of the intensity of the useful signal in the region of interest to the intensity of nonspecific background fluorescence. Materials and methods. The pancreas of three adult Wistar rats was fixed in Bouin solution (20 hours) and poured into paraplast after standard histological processing. The study was carried out on paraffin sections of the pancreas. The islets’ insulin and glucagon were determined by immunofluorescence method using monoclonal antibodies (Santa Cruz Biotechnology). The immunofluorescence reaction was studied using an AxioImager-M2 fluorescent microscope. AxioVision digital image analysis system was used for fluorescence imaging, and ImageJ 64-bit image analysis system was used for image quantification. 30 pancreatic islets with an area from 3000 µm2 to 5000 µm2 (8–13 % of the frame area) were analyzed. Results. Measurements carried out at constant values of hormone concentration in endocrinocytes showed a different estimate of the average fluorescence intensity for insulin and glucagon, which depended on the intensity of UV radiation. As the intensity of UV radiation increased, the average fluorescence intensity in the region of interest for insulin and glucagon increased, but when the camera exposure was corrected, it became almost the same. Regardless of this, the intensity of nonspecific background fluorescence increased monotonically. The use of the ratio of the logarithms of the background fluorescence of the drug and the fluorescence of endocrinocytes in the calculations gives a stable estimate of the relative concentration of hormones, which does not depend on the intensity of the selected UV radiation regime, as well as on the duration of UV irradiation of the drug. This makes it possible to neutralize the effect of photodynamic discoloration of the preparation caused by continuous irradiation. Methods for machine selection of the region of interest by various algorithms of the ImageJ program lead to different estimates of its area, integral, and average fluorescence values. At the same time, the result closest to the “ideal” interactive method of highlighting the area of interest for insulin and glucagon was shown by Otsu’s algorithm. Conclusions. In immunofluorescent examination of the pancreas, a moderate UV radiation mode should be selected, exposure correction of the CCD camera before taking each frame, and the total time for examining the visual field of the sample should be limited to 1–2 minutes. To highlight the area of interest for insulin and glucagon in automatic analysis, it is recommended to use the Otsu algorithm. To obtain a quantitative estimate of the average fluorescence intensity in the region of interest, it is recommended to use the ratio of the logarithms of the background fluorescence of the drug and endocrinocytes in the calculations.

Fullerenol Quantum Dots-Based Highly Sensitive Fluorescence Aptasensor for Patulin in Apple Juice.

A highly selective and sensitive aptasensor for detecting patulin (PAT) was constructed based on the fluorescence quenching of fullerenol quantum dots (FOQDs) towards carboxytetramethylrhodamine (TAMRA) through PET mechanism. The π-π stacking interaction between PAT aptamer and FOQDs closed the distance between TAMRA and FOQDs and the fluorescence of TAMRA was quenched with maximum quenching efficiency reaching 85%. There was no non-specific fluorescence quenching caused by FOQDs. In the presence of PAT, the PAT aptamer was inclined to bind with PAT and its conformation was changed. Resulting in the weak π-π stacking interaction between PAT aptamer and FOQDs. Therefore, the fluorescence of TAMRA recovered and was linearly correlated to the concentration of PAT in the range of 0.02–1 ng/mL with a detection limit of 0.01 ng/mL. This PAT aptasensor also performed well in apple juice with linear dynamic range from 0.05–1 ng/mL. The homogeneous fluorescence aptasensor shows broad application prospect in the detection of various food pollutants.

Confocal reflectance microscopy for metal and lipid nanoparticle visualization in the brain.

Aim: A requirement for nanoparticle (NP) research is visualization of particles within cells and tissues. Limitations of electron microscopy and low yields of NP fluorescent tagging warrant the identification of alternative imaging techniques. Method: Confocal reflectance microscopy (CRM) in combination with fluorescence imaging was assessed for visualizing rhodamine B-conjugated silver and fluorescein isothiocyanate-conjugated lipid core-stearylamine NP uptake in vitro and in vivo. Results: CRM successfully identified cellular uptake and blood-brain barrier penetration of NPs owing to their distinguishing refractive indices. NP-dependent reflectance signals in vitro were dose and incubation time dependent. Finally, CRM facilitated the distinction between nonspecific fluorescence signals and NPs. Conclusion: These findings demonstrate the value of CRM for NP visualization in tissues, which can be performed with a standard confocal microscope.

Sensing cellular metabolism in turbid media using spectral phasor analysis on UV-excited autofluorescence

Reduced nicotinamide adenine dinucleotide (NADH) and nicotinamide adenine dinucleotide phosphate (NADPH) are metabolic cofactors playing significant, distinct roles in cellular metabolism primarily involving cellular respiration and maintaining antioxidant defenses, respectively. Signals from NADH and NADPH are a significant component of cellular autofluorescence and are useful for metabolic sensing. For in vivo sensing of tissues, challenges include the presence of non-specific background fluorescence as well as perturbations of intrinsic NADH/NADPH fluorescence due to scattering and absorption.

The Problem of DNA/RNA Contamination in the Laboratory during PCR Testing for COVID-19

Introduction. When conducting PCR (polymerase chain reaction) testing of biospecimens for SARS-CoV-2 RNA at the beginning of the COVID-19 pandemic, the laboratory service in Russia and foreign countries encountered problems related to the accuracy of diagnostics and obtaining false negative, false positive, and dubious results. The objective of this work was to analyze current literature on the problem of false positive and dubious results of RT-PCR testing for COVID-19. Material and methods. We selected Russian and foreign English-language publications devoted to organization of laboratory diagnostics of the novel coronavirus disease, challenges of PCR testing for SARS and MERS, and general issues of DNA contamination in a PCR laboratory for 2012–2020. We also reviewed current regulations and guidelines for COVID-19 diagnostic testing. Results. The analysis of factors leading to contamination of specimens with nucleic acids in the laboratories performing massive COVID-19 PCR testing during the pandemic showed that the main reasons for contamination included a large number of tests, accumulation of samples in the laboratory, and the increased amount of wastes containing amplification products. Cross-contamination occurs due to technical errors in the course of laboratory manipulations at the stages of sample preparation and inactivation, RNA isolation, and addition of cDNA/RNA or positive control samples to the reaction mixture. Pollution of laboratory working areas with amplicons arising from the opening of tubes and plates containing PCR products is the main cause of total contamination in the laboratory. Signs of cross-contamination include the increase in the proportion of positive samples with low threshold cycle values and detection of a positive signal from negative control samples at RNA isolation and amplification stages. A positive result for all samples in a round, including negative control samples, is a marker of “total contamination” in the laboratory. In addition to contamination, formation of nonspecific PCR products at late reaction cycles and nonspecific fluorescence of the reaction mixture, which occurs when reagent storage temperatures are not observed, may also lead to false positive results. Conclusion. To prevent contamination in a PCR laboratory, strict control over the flow of test samples and medical wastes, regular analysis of the frequency of positive test results, and mandatory laboratory quality control of testing and DNA/RNA contamination are compulsory.

A single snapshot multiplex immunoassay platform utilizing dense test lines based on engineered beads

Co-circulation of coronavirus disease 2019 (COVID-19) and dengue fever has been reported. Accurate and timely multiplex diagnosis is required to prevent future pandemics. Here, we developed an innovative microfluidic chip that enables a snapshot multiplex immunoassay for timely on-site response and offers unprecedented multiplexing capability with an operating procedure similar to that of lateral flow assays. An open microchannel assembly of individually engineered microbeads was developed to construct nine high-density test lines, which can be imaged in a 1 mm2 field-of-view. Thus, simultaneous detection of multiple antibodies would be achievable in a single high-resolution snapshot. Next, we developed a novel pixel intensity-based imaging process to distinguish effective and non-specific fluorescence signals, thereby improving the reliability of this fluorescence-based immunoassay. Finally, the chip specifically identified and classified random combinations of arbovirus (Zika, dengue, and chikungunya viruses) and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) antibodies within 30 min. Therefore, we believe that this snapshot multiplex immunoassay chip is a powerful diagnostic tool to control current and future pandemics.

Peptoid microsphere coatings to improve performance in sandwich ELISA microarrays

Enzyme-linked immunosorbent assay (ELISA) microarray performance is limited by low assay sensitivity and dynamic range. Increasing the surface area for reagent binding can help to improve performance, but standard techniques such as roughening the surface or adding a polymer coating lead to increased non-specific fluorescence and do not have reproducibly improved performance. Another approach to increase surface area is adding a microsphere coating on the surface. Poly-N-substituted glycine (peptoid) microspheres are ideal for this application due to low immunogenicity, protease-resistance, and biocompatibility. Peptoids are polymers with a backbone similar to peptides, but with the side chains appended to nitrogen rather than the alpha carbon. A variety of side chain chemistries can be incorporated into peptoids through a solid-phase, sequence-specific synthesis protocol. Here we report the development of sandwich ELISA microarray on peptoid microsphere coated glass slides. Coating morphology was evaluated via SEM and efficacy was assessed by ELISA microarray performance. Peptoid microsphere coated glass slides exhibit an increase in signal intensity and dynamic range as compared to commercially available microarray slides. These studies show the potential for peptoid microspheres as coatings for ELISA microarray slides, as well as for use in other biosensor applications.