Nonspecific Dyes Research Articles

Identity confirmation of extracellular vesicles by capillary electrophoresis using non-specific dyes

Extracellular vesicles (EVs) are membrane-enveloped nanostructures secreted by prokaryotic and eukaryotic cells. Carrying a variety of essential components, EVs are involved in numerous biological processes including intercellular communication and immunological response. The characterization of extracellular vesicles with capillary electrophoresis (CE) faces several challenges. Due to the limited availability of commercial standards, the identity confirmation of the EV signal is among these issues. In the presented work, a method for identity confirmation of EVs by CE was developed. Identification was based on the application of non-specific dyes and fluorescence detection, and EVs obtained from Escherichia coli and citrus fruits (Citrus limon and Citrus aurantifolia) were used. It was found that the presented methodology effectively detects the cargo carried by EVs (including nucleic acids, proteins, and lipids) and enables the staining of subpopulations separated by CE. The strategy holds promise to be utilized for EV heterogeneity assessment.

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.

Visualizing NETosis Using a Novel Neutrophil Extracellular Trap-Specific Marker.

As the most abundant leukocyte in circulation, the neutrophil plays a far-reaching role in maintaining homeostasis. Within the context of disease, however, neutrophils can potentiate various pathophysiological mechanisms with disastrous consequences for patients. The role of the neutrophil in disease is complex with mechanisms like NETosis driving the progression of several pathologies. NETosis involves neutrophils extruding protein-decorated DNA webs called neutrophil extracellular traps (NETs), which facilitate the progression of inflammatory, non-infectious, and neoplastic pathologies. The need to visualize NETs has thus never been greater. Current approaches for visualizing NETs are limited in specificity and sensitivity, involving non-specific fluorescent DNA dyes or co-stains of neutrophil and DNA markers. Improved methodologies are needed to robustly distinguish NETs from other cell-free DNA. Excitingly, a novel NET-specific posttranslational modification involving cleavage on the N-terminus of histone H3 has recently been identified. Here, we demonstrate that this single marker is superior to the conventional use of the co-stain of the neutrophil marker, myeloperoxidase, and, the DNA marker, histone H3 citrullination in visualizing neutrophil NETosis. This is due to this single marker's unparalleled ability to identify, not only more NETs but also their formation at earlier stages of NETosis. Moreover, we additionally propose a stepwise mechanism of neutrophil NETosis in which a histone H3 cleavage event precedes histone H3 citrullination. Taken together, these results demonstrate a novel method for visualizing NETs, allowing for continued exploration of their multifaceted roles in immunity and disease.

Calcium Imaging of Anopheles coluzzii Mosquito Antennae Expressing the Calcium Indicator GCaMP6f.

Calcium imaging is a technique used to measure functional neuronal activities in response to stimuli. It has been used for years to study odorant-induced responses in insects (i.e., honeybees, Drosophila, and moths) and was recently introduced into mosquitoes. Traditionally, calcium imaging in mosquitoes was performed using nonspecific calcium indicator dyes to examine neuronal responses in whole insect brain regions, but the development of genetically encoded calcium indicators (GECIs) has facilitated the ability to perform functional calcium imaging on specific tissues. For example, by specifically expressing a GECI in olfactory neurons, the odor-induced responses of these neurons in peripheral organs can be examined. Calcium imaging of mosquito antennae further provides an advantageous method for simultaneously visualizing the activity of several antennal neurons in a single experiment. In this protocol, we describe a calcium imaging method to study odor-evoked responses in Anopheles coluzzii antennae expressing the calcium indicator GCaMP6f. This method requires imaging equipment (compound microscope, light sources, and camera), an odorant delivery system, and image acquisition software. The mosquito preparation is straightforward but requires practice to minimize mosquito movement during imaging. Recorded videos can be analyzed using Fiji software to generate heatmaps and activity traces for odorant-evoked responses. This protocol can also be used, with some modifications, to study other peripheral organs (such as labella, palps, and tarsi).

Fluorescence Molecular Targeting of Colon Cancer to Visualize the Invisible.

Colorectal cancer (CRC) is a common cause of cancer and cancer-related death. Surgery is the only curative modality. Fluorescence-enhanced visualization of CRC with targeted fluorescent probes that can delineate boundaries and target tumor-specific biomarkers can increase rates of curative resection. Approaches to enhancing visualization of the tumor-to-normal tissue interface are active areas of investigation. Nonspecific dyes are the most-used approach, but tumor-specific targeting agents are progressing in clinical trials. The present narrative review describes the principles of fluorescence targeting of CRC for diagnosis and fluorescence-guided surgery with molecular biomarkers for preclinical or clinical evaluation.

Synergetic dual-toehold mediated controllable transcription amplification for detecting lung cancer-related circulating miRNAs in blood

Circulating microRNAs (miRNAs) in blood are recognized as key biomarkers of cancers. Herein, taking advantage of the dynamic DNA nanotechnology, we report an assay to detect lung cancer-related circulating miRNAs in blood based on a synergetic dual-toehold mediated controllable transcription amplification (SMART). Unlike traditional single-toehold overhanging system with limited design flexibility, the synergetic dual-toehold exchange was employed to not only inhibit background signal, but also facilitate the downstream introducing of target-responsive isothermal amplification. This feature allows the SMART platform combines synergetic dual-toehold mediated strand displacement with transcription amplification. The SMART, acting as an effective signal transducer and amplifier, is thus able to ultrasensitively output the let-7a recognition event via significantly accumulating Broccoli RNA aptamers responsible for the binding with DFHBI-1 T. Moreover, the Broccoli/DFHBI-1 T reporter increases the signal-to-background ratio compared to that using non-specific nucleic acid dyes and eliminates the use of chemically labeled oligonucleotide probes. The experimental demonstration shows the SMART method realized the detection of let-7a lower into 10 fM, identification of let-7a from homologous and heterologous analogues, and profiling let-7a from clinical blood samples. This work improves the rational design of dynamic DNA devices-based signal isothermal in the fields of disease diagnosis and biomedical study.

Optimized cytotoxicity assay for co-suspended effector and target cells

In recent years, adoptive cell therapy of immune effector cells, such as chimeric antigen receptor-T (CAR-T) cells, natural killer (NK) cells, and epitope-specific cytotoxic T lymphocyte (CTL) cells have been employed in clinical trials. In addition, CD19 CAR-T cells have been approved by the FDA for treatment of non-Hodgkin lymphoma and diffuse large B-cell lymphoma. In this context, it is vital to detect cellular cytotoxicity and monitor the quality of ex vivo expanded immune cells before product release and patient infusion. Target cells could proliferate in parallel with effector cells during the cytotoxicity assay, making it difficult to estimate the death ratio using conventional approaches. Meanwhile, non-specific dyes or non-homogeneous biomarkers for target cells may interfere with the final readout post addition of effector cells. Here, we modified a component of the coincubation medium to suppress the spontaneous release of bis(acetoxymethyl)2,2′:6′,2″-terpyridine-6,6″-dicarboxylate and sustained the window at a stable range (~70%). Further, the optimized Eu-TDA method presented reliable outcomes compared with lactate dehydrogenase detection and was compatible with cytotoxicity tests for NK cells and specific CTLs. Finally, the reported assay can accurately detect death of target cells depending on the amount of hydrophilic complex and can be reliably applied in quality control and cell activity evaluation tests on co-suspended effector and target cells. SummaryA medium component for cellular coincubations (and associated protocols) have been optimized and validated for cytotoxicity assays, which can reliably evaluate the potency of engineered CD19 CAR-T cells, NK cells, and specific CTLs. In particular, the reported method can be applied widely in routine assays for bi-suspended effector and target cells with a stable window.

Tumor-specific near-infrared nanobody probe rapidly labels tumors in an orthotopic mouse model of pancreatic cancer

BackgroundNanobodies, derived from camelid antibodies made of only heavy chains, are the smallest, biologic, antigen-binding fragments (~15kDa) with faster pharmacokinetics and better tumor penetration efficiency than standard antibodies. The present study evaluates the efficacy of a fluorescent, anti-carcinoembryonic antigen (CEA) nanobody for rapid tumor labeling in an orthotopic mouse model of pancreatic cancer. MethodsAnti-CEA or control nanobodies were conjugated with the near-infrared fluorophore IRDye 800CW. Fragments of BxPC-3 (high-CEA expressing) or MiaPACA-2 (low-CEA expressing) human pancreatic cancer cell lines were orthotopically implanted into the pancreatic tail of nude mice. After tumors reached 7 to 10 mm in size, 2 nmol anti-CEA or control nanobody-IRDye800CW were injected intravenously. Mice were imaged at various time points hours post-injection. ResultsAnti-CEA nanobodies clearly labeled BxPC3 orthotopic pancreatic tumors 3 hours after injection. The signal was present as early as 15 minutes after injection and was robust at 1 to 3 hours after injection with a tumor-to-background ratio of 2.66. In contrast, there was very low accumulation in the low CEA-expressing, MiaPACA2 pancreatic orthotopic tumors. The fluorophore-conjugated nanobody was specific for CEA-expressing tumors, while the control nanobody did not show any tumor-specific signal. Both nanobodies had strong kidney uptake as expected for small-molecule probes. The fluorescence signal was detectable using 2 clinical, Food and Drug Administration-approved, 800 nm imaging devices as well as small animal imaging systems. ConclusionThis anti-CEA, nanobody-based, fluorescent probe labeled pancreatic orthotopic tumors within 15 minutes of intravenous injection. Fluorescent anti-CEA nanobodies have labeling kinetics that approach the speed of nonspecific dyes such as indocyanine green but with the specificity of antibodies. The use of fluorescently-labeled, intact antibodies leads to a labeling delay of 48 to 96 hours between probe administration and the necessarily delayed time of operation, which can be avoided with nanobodies. The kinetics of a nanobody-based probe makes it a practical agent for same-day, patient administration and fluorescence-guided surgery.

Real-time Detection and Monitoring of Loop Mediated Amplification (LAMP) Reaction Using Self-quenching and De-quenching Fluorogenic Probes

Loop-mediated isothermal amplification (LAMP) is an isothermal nucleic acid amplification (iNAAT) technique known for its simplicity, sensitivity and speed. Its low-cost feature has resulted in its wide scale application, especially in low resource settings. The major disadvantage of LAMP is its heavy reliance on indirect detection methods like turbidity and non-specific dyes, which often leads to the detection of false positive results. In the present work, we have developed a direct detection approach, whereby a labelled loop probe quenched in its unbound state, fluoresces only when bound to its target (amplicon). Henceforth, referred to as Fluorescence of Loop Primer Upon Self Dequenching-LAMP (FLOS-LAMP), it allows for the sequence-specific detection of LAMP amplicons. The FLOS-LAMP concept was validated for rapid detection of the human pathogen, Varicella-zoster virus, from clinical samples. The FLOS-LAMP had a limit of detection of 500 copies of the target with a clinical sensitivity and specificity of 96.8% and 100%, respectively. The high level of specificity is a major advance and solves one of the main shortcomings of the LAMP technology, i.e. false positives. Self-quenching/de-quenching probes were further used with other LAMP primer sets and different fluorophores, thereby demonstrating its versatility and adaptability.

Gene expression studies of reference genes for quantitative real-time PCR: an overview in insects.

Whenever gene expression is being examined, it is essential that a normalization process is carried out to eliminate non-biological variations. The use of reference genes, such as glyceraldehyde-3-phosphate dehydrogenase, actin, and ribosomal protein genes, is the usual method of choice for normalizing gene expression. Although reference genes are used to normalize target gene expression, a major problem is that the stability of these genes differs among tissues, developmental stages, species, and responses to abiotic factors. Therefore, the use and validation of multiple reference genes are required. This review discusses the reasons that why RT-qPCR has become the preferred method for validating results of gene expression profiles, the use of specific and non-specific dyes and the importance of use of primers and probes for qPCR as well as to discuss several statistical algorithms developed to help the validation of potential reference genes. The conflicts arising in the use of classical reference genes in gene normalization and their replacement with novel references are also discussed by citing the high stability and low stability of classical and novel reference genes under various biotic and abiotic experimental conditions by employing various methods applied for the reference genes amplification.

Comprehensive phantom for interventional fluorescence molecular imaging.

Fluorescence imaging has been considered for over a half-century as a modality that could assist surgical guidance and visualization. The administration of fluorescent molecules with sensitivity to disease biomarkers and their imaging using a fluorescence camera can outline pathophysiological parameters of tissue invisible to the human eye during operation. The advent of fluorescent agents that target specific cellular responses and molecular pathways of disease has facilitated the intraoperative identification of cancer with improved sensitivity and specificity over nonspecific fluorescent dyes that only outline the vascular system and enhanced permeability effects. With these new abilities come unique requirements for developing phantoms to calibrate imaging systems and algorithms. We briefly review herein progress with fluorescence phantoms employed to validate fluorescence imaging systems and results. We identify current limitations and discuss the level of phantom complexity that may be required for developing a universal strategy for fluorescence imaging calibration. Finally, we present a phantom design that could be used as a tool for interlaboratory system performance evaluation.

Advancing Surgical Vision with Fluorescence Imaging.

Surgical success depends on the accuracy with which disease and vital tissue can be intraoperatively detected. However, the dominant visualization approach, i.e., human vision, does not see under the tissue surface and operates on low contrast between sites of disease, such as cancer, and the surrounding tissue. Intraoperative fluorescence imaging is emerging as a highly effective method to improve surgical vision and offers the potential to be intergrated seamlessly into the normal workflow of the operating room without causing disruption or undue delay. We review and compare two critical fluorescence imaging directions: one that uses nonspecific fluorescence dyes, addressing tissue perfusion and viability, and one that uses targeted agents, interrogating pathophysiological features of disease. These two approaches present detection sensitivity challenges that may differ by orders of magnitude and require different detection strategies. Nevertheless, fluorescence imaging provides the surgeon with previously unavailable real-time feedback that improves surgical precision and can become essential for interventional decision-making.

Handheld confocal laser endomicroscopic imaging utilizing tumor-specific fluorescent labeling to identify experimental glioma cells in vivo.

Background:We have reported that handheld confocal laser endomicroscopy (CLE) can be used with various nonspecific fluorescent dyes to improve the microscopic identification of brain tumor and its boundaries. Here, we show that CLE can be used experimentally with tumor-specific fluorescent labeling to define glioma margins in vivo.Methods:Thirteen rats underwent craniectomy and in vivo imaging 21 days after implantation with green fluorescent protein (GFP)-labeled U251 (n = 7) cells or epidermal growth factor receptor (EGFR) overexpressing F98 cells (n = 6). Fluorescein isothiocyanate (FITC) conjugated EGFR fluorescent antibody (FITC-EGFR) was applied for contrast in F98 tumors. Confocal images of normal brain, obvious tumor, and peritumoral zones were collected using the CLE system. Bench-top confocal microscopy and hematoxylin and eosin-stained sections were correlated with CLE images.Results:GFP and FITC-EGFR fluorescence of glioma cells were detected by in vivo visible-wavelength fluorescence CLE. CLE of GFP-labeled tumors revealed bright individual satellite tumor cells within peritumoral tissue, a definitive tumor border, and subcellular structures. Imaging with FITC-EGFR labeling provided weaker contrast in F98-EGFR tumors but was able to delineate tumor cells. Imaging with both methods in various tumor regions correlated with standard confocal imaging and clinical histology.Conclusions:These data suggest that in vivo CLE of selectively tagged neoplasms could allow specific interactive identification of tumoral areas. Imaging of GFP and FITC-EGFR provides real-time histologic information precisely related to the site of microscopic imaging of tumor.

Ethyl chitosan synthesis and quantification of the effects acquired after grafting it on a cotton fabric, using ANOVA statistical analysis

Three ethyl chitosans (ECSs) have been prepared using the ethyl chloride (AA) that was obtained in situ. Each ECS was applied on a 100% cotton fabric through a pad–dry–cure technology. Using the ANOVA as statistic method, the wrinkle-proofing effects have been determined varying the concentrations of AA (0.1–2.1mmol) and chitosan (CS) (0.1–2.1mmol). Alkylation and grafting mechanisms have been confirmed by the results of FTIR, 1H NMR, XPS, SEM, DSC and termogravimetric analyses. The performances of each ECS as wrinkle-proofing agent have been revealed through quantitative methods (taking-up degree, wrinkle-recovering angle, tensile strength and effect's durability). The ECSs confer wrinkle-recovering angle and tensile strength higher than those of the witness sample. Durability of ECSs grafted on cotton have been demonstrated by a good capacity of dyeing with non-specific (acid/anionic and cationic) dyes under severe working conditions (100°C, 60min) and a good antimicrobial capacity.

Combination of Free Software, Light Microscopy and Non-specific Dyes for a High-throughput Analysis in Live/Dead Cell Count

Combination of Free Software, Light Microscopy and Non-specific Dyes for a High-throughput Analysis in Live/Dead Cell Count

A reproducible differential blood cell count without a cytometer or specific markers

Abstract Introduction: A differential blood cell count represents a substantial component of the daily clinical routine. The aim of this study was to conduct automated high-throughput analyses of light microscopy images of leukocytes with unspecific staining (hematoxylin-eosin, HE) and to classify the resulting subgroups (lymphocytes, monocytes and neutrophils). Materials and Method: The software package CellProfiler was used for the image analysis and cell classification. The results were compared to those from hematological laboratories that analyzed the same samples. Results: There was a high similarity between the results obtained by image analysis and those from the hematological laboratories, with an r2=0.95 for the differential count and an r2=0.89 for the total count. Conclusion: Differential blood cell count using light microscopy, nonspecific dyes and advanced image analysis is accurate, reproducible, and less expensive compared to other techniques. The results also showed a strong correlation when compared to traditional methods.

Tinctorial Response of Recycled PET Fibers to Chemical Modifications during Saponification and Aminolysis Reactions

In this article we show that poly(ethylene terephthalate) (PET) fibers obtained from the recycling process of PET bottles can be chemically modified and used to create materials destined to become clothing articles. The modifications of the characteristics of PET fibers through saponification and aminolysis reactions have been studied. The work represents a comparative study of the behavior of PET virgin (of synthesis) fibers versus recycled PET fibers (from PET bottles). Comparisons have been made between the modifications which appear in physical and chemical structures, thermal stability, mechanical properties, and dyeability under the action of some reactions with NaOH, with ethylene diamine, or with their mixture at 20 °C. The FTIR, SEM, EDAX, XRD, DSC, and TGA analyses made evident the differences/similarities between the two types of studied polyester fibers. The recycled PET fibers are much less crystalline, more stable at high temperature, and easier to dye with nonspecific (anionic and cationic) dyes. After the treatment with AgNO3, the virgin/recycled PET fibers, chemically modified (which have NH2 groups), have antimicrobial activities due to their affinity for Ag ions. The silver presence on the treated samples can be seen even after 10 cycles of repeated home laundering. The only inconvenience of the treatments meant to modify the PET chemical structure is tenacity diminution, manifested in different ways, depending on the reagent type, concentration, and duration. However, the recycled PET fibers can be used to create materials destined to become clothing articles (by themselves or blended with synthetic/natural fibers) which can be more easily and more economically dyed in a single bath and a single stage.

Holoparasitic Rafflesiaceae possess the most reduced endophytes and yet give rise to the world's largest flowers

Species in the holoparasitic plant family Rafflesiaceae exhibit one of the most highly modified vegetative bodies in flowering plants. Apart from the flower shoot and associated bracts, the parasite is a mycelium-like endophyte living inside their grapevine hosts. This study provides a comprehensive treatment of the endophytic vegetative body for all three genera of Rafflesiaceae (Rafflesia, Rhizanthes and Sapria), and reports on the cytology and development of the endophyte, including its structural connection to the host, shedding light on the poorly understood nature of this symbiosis. Serial sectioning and staining with non-specific dyes, periodic-Schiff's reagent and aniline blue were employed in order to characterize the structure of the endophyte across a phylogenetically diverse sampling. A previously identified difference in the nuclear size between Rafflesiaceae endophytes and their hosts was used to investigate the morphology and development of the endophytic body. The endophytes generally comprise uniseriate filaments oriented radially within the host root. The emergence of the parasite from the host during floral development is arrested in some cases by an apparent host response, but otherwise vegetative growth does not appear to elicit suppression by the host. Rafflesiaceae produce greatly reduced and modified vegetative bodies even when compared with the other holoparasitic angiosperms once grouped with Rafflesiaceae, which possess some vegetative differentiation. Based on previous studies of seeds together with these findings, it is concluded that the endophyte probably develops directly from a proembryo, and not from an embryo proper. Similarly, the flowering shoot arises directly from the undifferentiated endophyte. These filaments produce a protocorm in which a shoot apex originates endogenously by formation of a secondary morphological surface. This degree of modification to the vegetative body is exceptional within angiosperms and warrants additional investigation. Furthermore, the study highlights a mechanical isolation mechanism by which the host may defend itself from the parasite.

Comparison of SYBR Green and TaqMan methods in quantitative real-time polymerase chain reaction analysis of four adenosine receptor subtypes.

Background:Real-time polymerase chain reaction (PCR) is based on the revolutionary method of PCR. This technique is the result of PCR enormous sensitivity and real-time monitoring combination. In quantitative gene expression analysis, two methods have more popularity, SYBR Green and TaqMan, SYBR Green is relatively cost benefit and easy to use and technically based on binding the fluorescent dye to double-stranded deoxyribonucleic acid (dsDNA) where TaqMan method has more expensive and based on dual labeled oligonucleotide and exonuclease activity of Taq polymerase enzyme. Specificity is the most important concern with the usage of any non-specific dsDNA-binding Dyes such as SYBR Green whiles more specificity showed by labeled oligonucleotide method such as TaqMan. In this study, we compared two common RT PCR methods, TaqMan and SYBR Green in measurement gene expression profile of adenosine receptors.Materials and Methods:Gene expression profiles of A1, A2A, A2B and A3 Adenosine receptors were analyzed by optimized TaqMan and SYBR Green quantitative RT PCR in breast cancer tissues. Primary expression data was normalizing by B. actin reference gene.Results:Efficiencies were calculated more than 95% for TaqMan and SYBR Green methods in all genes. The correlations between means of normalized data of each gene in two methods were positive and significant (P < 0.05).Conclusion:Data analysis showed that with the use of high performance primer and by use proper protocols and material we can make precise data by SYBR Green as TaqMan method. In other word by optimization of SYBR Green method, its performance and quality could be comparable to TaqMan method.

Coherent anti-Stokes Raman scattering for label-free biomedical imaging

Coherent anti-Stokes Raman scattering (CARS) has established itself as an imaging technique capable of providing video-rate imaging of biological specimens through vibrational coherence of endogenous molecules. Current techniques predominantly involve the application of costly, invasive and potentially non-specific dyes or labels for imaging biomolecules. CARS microscopy can however provide a high-resolution and non-invasive alternative for imaging biomolecules of interest without the need for exogenous labels. Here we provide an overview of CARS including the technique and common instrumentation as well as its applications in biomedical imaging. We discuss the major biomedical areas where CARS has been applied such as in evaluating liver disease, progression of atherosclerosis, tumour classification and tracking drug delivery, whilst also assessing the future challenges for clinical translation.