Identification of Unambiguous Borrelia Peptides in Human Urine Using Affinity Capture and Mass Spectrometry.

The combination of advanced mass spectrometry and enrichment-based sample preparation methods has enhanced analytical capabilities in clinical proteomics. In this chapter, we describe a method of proteome analysis to identify Borrelia-derived peptides in urine that includes a sample affinity enrichment method coupled with liquid chromatography tandem mass spectrometry analysis and a bioinformatic peptide authentication algorithm.

Description of the neuroanatomy of the brachial plexus in South American lizards. Phylogenetic implications.

Few studies considered the anatomy of the nerve plexuses and musculature associated with them in ectothermic sauropsids. Based on differentiated Sudan Black B staining and conventional dissections, we describe the neuroanatomy of the brachial plexus, its main associated nerves, and muscles. For that, representatives of the genera Diplolaemus, Liolaemus, Phymaturus, and Tropidurus were selected. Based on this, potentially useful characters for phylogenetic analysis were described. Our results show that the brachial plexus can be formed by four, five, or six nerve branches. The brachial flexor trunk, circumflex, interosseous, median, radial, subscapulocoracoid, supracoracoid, and ulnar nerves were identified. Regarding the muscles innervated by the main nerves, the following muscles were identified: biceps brachii, deltoideus scapularis, latissimus dorsi, levator scapulae, pectoralis, serratus thoracis, trapezius, triceps longus caudalis, and triceps longus lateralis. Phylogenetic analyzes revealed 31 potential synapomorphies. There exists evidence that neuroanatomy studies in a phylogenetic context could provide useful information helping to elucidate the relationships between taxonomic groups.

Blocking autofluorescence in brain tissues affected by ischemic stroke, hemorrhagic stroke, or traumatic brain injury.

Autofluorescence is frequently observed in animal tissues, interfering with an experimental analysis and leading to inaccurate results. Sudan black B (SBB) is a staining dye widely used in histological studies to eliminate autofluorescence. In this study, our objective was to characterize brain tissue autofluorescence present in three models of acute brain injury, including collagenase-induced intracerebral hemorrhage (ICH), traumatic brain injury (TBI), and middle cerebral artery occlusion, and to establish a simple method to block autofluorescence effectively. Using fluorescence microscopy, we examined autofluorescence in brain sections affected by ICH and TBI. In addition, we optimized a protocol to block autofluorescence with SBB pretreatment and evaluated the reduction in fluorescence intensity. Compared to untreated, pretreatment with SBB reduced brain tissue autofluorescence in the ICH model by 73.68% (FITC), 76.05% (Tx Red), and 71.88% (DAPI), respectively. In the TBI model, the ratio of pretreatment to untreated decreased by 56.85% (FITC), 44.28% (Tx Red), and 46.36% (DAPI), respectively. Furthermore, we tested the applicability of the protocol using immunofluorescence staining or Cyanine-5.5 labeling in the three models. SBB treatment is highly effective and can be applied to immunofluorescence and fluorescence label imaging techniques. SBB pretreatment effectively reduced background fluorescence but did not significantly reduce the specific fluorescence signal and greatly improved the signal-to-noise ratio of fluorescence imaging. In conclusion, the optimized SBB pretreatment protocol blocks brain section autofluorescence of the three acute brain injury models.

Sudan Black B Pretreatment to Suppress Autofluorescence in Silk Fibroin Scaffolds.

Natural polymers are extensively utilized as scaffold materials in tissue engineering and 3D disease modeling due to their general features of cytocompatibility, biodegradability, and ability to mimic the architecture and mechanical properties of the native tissue. A major limitation of many polymeric scaffolds is their autofluorescence under common imaging methods. This autofluorescence, a particular challenge with silk fibroin materials, can interfere with the visualization of fluorescently labeled cells and proteins grown on or in these scaffolds, limiting the assessment of outcomes. Here, Sudan Black B (SBB) was successfully used prefixation prior to cell seeding, in various silk matrices and 3D model systems to quench silk autofluorescence for live cell imaging. SBB was also trialed postfixation in silk hydrogels. We validated that multiple silk scaffolds pretreated with SBB (hexafluoro-2-propanol-silk scaffolds, salt-leached sponges, gel-spun catheters, and sponge-gel composite scaffolds) cultured with fibroblasts, adipose tissue, neural cells, and myoblasts demonstrated improved image resolution when compared to the nonpretreated scaffolds, while also maintaining normal cell behavior (attachment, growth, proliferation, differentiation). SBB pretreatment of silk scaffolds is an option for scaffold systems that require autofluorescence suppression.

Sudan Black B treatment for reducing autofluorescence in human glioma tissue and improving fluorescent signals of bacterial LPS staining.

The 3D visualization based on tissue clearing technology allows us to have a deeper understanding of the 3D spatial information of deep molecules in the tissue. Tissue clearing and bacterial labeling methods have been used for in situ 3D microbiota imaging, and we have developed a pipeline for 3D visualization of in situ microbiota in human gliomas. Anti-LPS antibodies are appropriate to label and characterize bacteria in situ within tumors. However, autofluorescence (AF) is common in biological tissues, especially in brain tissues filled with lipofuscin-like (LF) substances. This natural fluorescent signal is usually considered to be a problem because it affects the 3D visualization of fluorescent signals in bacterial LPS staining. Here, we used Sudan Black B (SBB) to mask the AF of human glioma tissue and explored in detail the optimal quencher concentration, which allows 3D visualization of intratumoral bacteria to reduce AF and maintain the intensity of intratumoral bacteria-specific LPS fluorescent signals.

Lipofuscin labeling through biorthogonal strain-promoted azide-alkyne cycloaddition for the detection of senescent cells.

A new method for senescent cell detection is described, which is based on lipofuscin labeling with a fluorescent reporter through a biorthogonal strain-promoted azide-alkyne cycloaddition. The sensing protocol involves a first step where the interaction of lipofuscin with a Sudan Black B derivative containing an azide moiety (SBB-N3 ) is carried out. In the final step, the azide moiety reacts with a fluorophore containing a cyclooctene ring (BODIPY). The efficacy of this two-step protocol is assessed in senescent melanoma SK-MEL-103 cells, senescent triple-negative breast cancer MDA-MB-231 cells and senescent WI-38 fibroblasts. In all cases, a clear fluorescence pattern was observed in senescent cells, compared to proliferative cells, only when the SBB-N3 -BODIPY probe was formed. Our results provide an alternative tool for the detection of senescent cells, based on an in situ bio-orthogonal reaction for lipofuscin labeling.

Reduction of autofluorescence in whole adult worms of Schistosoma japonicum for immunofluorescence assay.

Immunofluorescence assay is one of methods to understand the spatial biology by visualizing localization of biomolecules in cells and tissues. Autofluorescence, as a common phenomenon in organisms, is a background signal interfering the immunolocalization assay of schistosome biomolecules, and may lead to misinterpretation of the biomolecular function. However, applicable method for reducing the autofluorescence in Schistosoma remains unclear. In order to find a suitable method for reducing autofluorescence of schistosomes, different chemical reagents, such as Sudan black B (SBB), trypan blue (TB), copper sulfate (CuSO4), Tris-glycine (Gly), and ammonia/ethanol (AE), at different concentrations and treatment time were tested, and SBB and CuSO4 were verified for the effect of blocking autofluorescence in immunofluorescence to localize the target with anti-SjCRT antibody. By comparing the autofluorescence characteristics of different conditions, it was found that SBB, TB and CuSO4 had a certain degree of reducing autofluorescence effect, and the best effect in females was using 50 mM CuSO4 for 6 h and in males was 0.5% SBB for 6 h. Furthermore, we have applied the optimized conditions to the immunofluorescence of SjCRT protein, and the results revealed that the immunofluorescence signal of SjCRT was clearly visible without autofluorescence interference. We present an effective method to reduce autofluorescence in male and female worm of Schistosoma japonicum for immunofluorescence assay, which could be helpful to better understand biomolecular functions. Our method provides an idea for immunofluorescence assay in other flukes with autofluoresence.

Methods to Study Myc-Regulated Cellular Senescence: An Update.

Cellular senescence plays a role in several physiological processes including aging, embryonic development, tissue remodeling, and wound healing and is considered one of the main barriers against tumor development. Studies of normal and tumor cells both in culture and in vivo suggest that MYC plays an important role in regulating senescence, thereby contributing to tumor development. We have previously described different common methods to measure senescence in cell cultures and in tissues. Unfortunately, there is no unique marker that unambiguously defines a senescent state, and it is therefore necessary to combine measurements of several different markers in order to assure the correct identification of senescent cells. Here we describe protocols for simultaneous detection of multiple senescence markers in situ, a quantitative fluorogenic method to measure senescence-associated ß-galactosidase activity (SA-ß-gal), and a new method to detect senescent cells based on the Sudan Black B (SBB) analogue GL13, which is applicable to formalin-fixed paraffin-embedded tissues. The application of these methods in various systems will hopefully shed further light on the role of MYC in regulation of senescence, and how that impacts normal physiological processes as well as diseases and in particular cancer development.

Neuroanatomy of the lumbosacral plexus in a highly diversified clade of South-American lizards. Evolution and phylogenetic implications.

Only few published studies that describe the neuroanatomy of lizards. Here, we describe the neuroanatomy of several Iguanian species belonging to three families (species of Liolaemus and Phymaturus belonging to Liolaemidae, Tropidurus and Stenocercus as representatives of Tropiduridae, and Diplolaemus as a representative of Leiosauridae). Based on Sudan Black B staining and conventional dissections, the neuroanatomy of the lumbosacral region is described. Among the most outstanding results is the existence of a neuronal pattern of the lumbosacral plexus characteristic of Liolaemidae. In addition, it was found that in the genus Liolaemus the lumbosacral plexus is composed of five pairs of spinal nerves while in Phymaturus, Tropidurus, Stenocercus and Diplolaemus is composed from five to six pairs of spinal nerves (from pre-sacral, sacral, and caudal vertebrae). We find differences in the origin of the spinal nerves that constitute the plexus. In some cases, the pattern of nerves involved includes even the caudal vertebrae. Variation among taxa related to the zeugopodial innervation is described, and the homology of these nervous branches is discussed. Sexual differences were found in some species studied. Based on our results and available literature, we found three different patterns of innervation of the zeugopodium. The major contribution of this study is to provide a detailed description of lumbosacral plexus nerves pathways from their origins at the vertebral column to the muscles that they innervate.

Sudan black B reducing the intestinal autofluorescence of rats and its application in immunofluorescence / 解剖学报

Objective To develop a feasible method to reduce the rat intestinal autofluorescence (AF). Methods Five rats were sacrificed. After cryostat section, intestinal AF was investigated by immunofluorescence (IF) before and after Sudan black B (SBB) treatment. Results The AF within the different rat intestinal segments was easily detected in both FITC- and TRITC- channel spectrum, which was not affected by serum blocking. After 0. 3% SBB treatment for 10 minutes, a significant reduction of AF was observed in the rat intestinal tissue. Moreover, the SBB treatment did not affect the expression of CD45 in the rat intestine detected by IF staining, but reduced the AF remarkedly. Conclusion The AF in rat intestinal frozen section can be effectively reduced with 0. 3% SBB treatment for 10 minutes.

An Alternative to Dye-Based Approaches to Remove Background Autofluorescence From Primate Brain Tissue.

Brain tissue contains autofluorescing elements that potentially impede accurate identification of neurons when visualized with fluorescent microscopy. Age-related accumulation of molecules with autofluorescent properties, such as lipofuscin, can possess spectral profiles that invade the typical emission range of fluorophores commonly utilized in fluorescent microscopy. The traditional method for accounting for this native fluorescence is to apply lipophilic dyes that are able to sequester these unwanted signals. While effective, such dyes can present a range of problems including the obstruction of fluorescent probe emissions. The present study utilizes aged primate midbrain tissue stained for tyrosine hydroxylase and calbindin to investigate an image processing approach for removing autofluorescence utilizing spectral imaging and linear unmixing. This technique is then compared against the traditional, dye-based autofluorescence sequestration method using Sudan Black B (SBB). Spectral imaging and linear unmixing yielded significantly higher cell numbers than SBB treatment. This finding suggests that computational approaches for removing autofluorescence in neural tissue are both viable and preferential to dye-based approaches for estimation of cell body numbers.

An investigation for recovery of polyhydroxyalkanoates (PHA) from Bacillus sp. BPPI-14 and Bacillus sp. BPPI-19 isolated from plastic waste landfill.

Bio-plastic synthesis from renewable and cheap agro-based materials is a sustainable solution for replacing conventionally produced plastic with environmental contamination. The current study was aimed at screening and characterization of Polyhydroxyalkanoates (PHA) producing bacterial isolates, evaluation of their potential and recovery of PHA using the isolates. The PHA compounds were characterized using FT-IR. Based on 16SrRNA sequence analyses the isolates were designated as Bacillus sp. BPPI-14 and Bacillus sp. BPPI-19. The isolates were gram-positive, rod-shaped, endospore former, and citrate test positive. Intracellular PHA granules were observed when these isolates were stained with Sudan black B (SBB) and Nile blue A (NBA) preliminary and specific staining dyes, respectively. Effect of pH, temperature and carbon sources on the PHA production by the isolates BPPI-14 and BPPI-19 was studied. Maximum PHA production was recorded for Glucose (49.46±2.79%) by Bacillus sp. BPPI-14 and followed by molasses (45.86±2.17%) by Bacillus sp. BPPI-19, respectively at 37°C and pH7. The obtained PHA polymers were confirmed by preparation of plastic films for both the isolates. Fourier transform infrared spectrum for BPPI-14 and BPPI-19 showed the peak (carboxylic acid group) at 1706-1719.39cm-1 was a characteristic feature of PHA and corresponds functional group (C=O).

Immunofluorescence Procedure for Developing Enamel Tissues.

Immunofluorescence (IF) labeling is a powerful technique that can provide a wealth of information on structural organization, supramolecular composition, and functional properties of cells and tissues. At the same time, nonspecific staining and false positives can seriously compromise IF studies and lead to confusing or even misleading results. It is particularly true for the extracellular matrix component of forming enamel. Here, we present an optimized IF protocol for developing enamel. Autofluorescence blocking by Sudan Black B (SBB) and establishing of proper isotype controls lead to a significant artifact reduction and improve reliability of the IF data.

Rapid and quantitative detection of trace Sudan black B in dyed black rice by surface-enhanced Raman spectroscopy (SERS).

The use of Sudan black B as coloring agent in foods is forbidden for its toxicology effect on human organs. This work proposes an efficient and sensitive method for food security inspection targeting Sudan black B. Surface-enhanced Raman spectroscopy (SERS) is applied to the analysis of trace Sudan black B. It could be detected at concentrations as low as 0.05 mg/L in standard solutions and 0.1 mg/kg in black rice extracts with the SERS method for measurement. The linear relationship between the intensity and concentration could be used for the quantitative detection of Sudan black B. The relation between dyeing time of black rice stained by Sudan black B solution and SERS intensity was studied which indirectly showed the effectiveness of the extraction method we designed. The results of the quantitative analysis reveal the practicability of using this method to detect Sudan black B in black rice. As a rapid and sensitive detection method, SERS can be extended to detect other food products and has a great application prospect in food safety inspection.

Spectral Characteristics of Autofluorescence in Renal Tissue and Methods for Reducing Fluorescence Background in Confocal Laser Scanning Microscopy.

Significant autofluorescence (AF) of renal tissue is one of the major causes restricting the use of immunofluorescent staining. This study aimed at controlling renal tissue AF and testing an effective method for optimizing specific signals. In the present study, we observed emergence of strong AF in all renal cells under different fluorescent channels. Significant concentration-dependent reduction in AF of kidney tissue was observed with the use of sodium borohydride (NaBH4) and Sudan black B (SBB) alone (p < 0.05). Under maximum effective concentration, semi-quantitative analysis revealed that inhibitory effect of SBB on AF was superior to that of NaBH4 (P < 0.01). When the two chemicals were combined, we observed that background can be reduced, and specific staining can be optimized at optimum concentration. Intensity of renal tissue was examined by confocal λ scanning, which showed that peaks were located at the range of approximately 480 - 590 nm and similar to those of flavin and lipofuscin. These results indicated that combined use of NaBH4 and SBB, when targeted at different sources of AF in renal tissue, is the most effective means of reducing background and preserving specificity of fluorescent labels. In addition, this method does not interfere with various steps of immunofluorescence experiments.

Autofluorescence: A potential pitfall in immunofluorescence-based inflammation grading.

Immunofluorescence (IF) staining of paraffin-embedded tissues is a frequently used method to answer research questions or even detect the abundance of a certain protein for diagnostic use. However, the signal originating from specific antibody-staining might be distorted by autofluorescence (AF) of the assessed tissue. Although the AF phenomenon is well known, its presence is often neglected by insufficient staining controls. In this study, we describe the existence of cellular AF in paraffin-embedded healthy and inflamed human and murine colonic tissues and present ways to reduce AF. The AF signal is detectable at emission spectra from 425 nm-738 nm, upon excitation from 403.6-638.7 nm and appears more pronounced in inflamed tissues. Most signals are located subepithelially in the tissue and in blood vessels. Previous studies have shown that the AF signals are caused by lipofuscin, which accumulates in lamina propria immune cells. In murine small intestine AF signals are present in granules in the Paneth cell zone. For alleviation of the AF signal, sudan black b (SBB) or copper sulfate was used. Incubation of the tissue slices with either one of the substances reduced AF. In conclusion, AF appears as an intrinsic biomarker for colonic inflammation. The dominant existence of AF in immune cells of IBD tissue elucidates the importance of negative controls and the limitation of IF staining for potential diagnostic purposes.

Waterborne Polyurethane Coatings with Covalently Linked Black Dye Sudan Black B.

Colored waterborne polyurethanes have been widely used in paintings, leathers, textiles, and coatings. Here, a series of black waterborne polyurethanes (WPUs) with different ratios of black dye, Sudan Black B (SDB), were prepared by step-growth polymerization. WPU emulsions as obtained exhibit low particle sizes and remarkable storage stability at the same time. At different dye loadings, essential structural, statistical and thermal properties are characterized. FTIR (fourier transform infrared) spectra indicate that SDB is covalently linked into waterborne polyurethane chains. All of the WPUs with covalently linked SDB show better color fastness and resistance of thermal migration than those with SDB mixed physically. Besides, WPUs incorporated SDB covalently with different polymeric diols, polytetramethylene ether glycol (PTMG), polypropylene glycol (PPG), poly-1, 4-butylene adipate glycol (PBA) and polycaprolactone glycol (PCL), were prepared to obtain different properties to cater to a variety of practical demands. By a spraying method, the black WPUs can be directly used as metal coatings without complex dyeing process by simply mixing coating additive and other waterborne resins, which exhibit excellent coating performance.

Optimizing Immunostaining of Enamel Matrix: Application of Sudan Black B and Minimization of False Positives from Normal Sera and IgGs.

Non-specific fluorescence from demineralized enamel matrix can significantly compromise the immunofluorescence studies and lead to false positives. Our goal was to assess degrees of non-specific binding under different conditions and try to optimize procedures for immunofluorescence studies of forming enamel. Firstly, we compared two methods for background fluorescence elimination, i.e., sodium borohydride and Sudan Black B treatments. The results demonstrated that Sudan Black B is far superior to sodium borohydride in reducing the background fluorescence in dental tissues. We also studied the extent of non-specific binding of normal sera and purified polyclonal immunoglobulins (IgG) from five mammalian species, guinea pig, rat, rabbit, goat, and sheep, over a broad range of dilutions. For all sera tested fluorescence signals increased exponentially from 1:1000 to 1:100. Interestingly, the non-specific binding of sera from rodent species was below that of positive control in the whole range of dilutions. In contrast, incubation with sera from 3 non-rodent species produced much higher signals which surpassed the positive control signal at 1:250~1:500 dilution range. Most of the IgGs didn't show significant non-specific binding within 0.25-5 µg/ml range, except rabbit IgG which demonstrated extremely high affinity to the enamel matrix even at concentrations as low as 1 µg/ml. Further, studies confirmed that Fab fragments of purified normal rabbit IgG, not conserved Fc fragments, were involved in the interactions. Our observations suggest this high affinity is associated with the antigen binding sites of rabbit IgG. We anticipate that our results will help enamel researchers to optimize and standardize their immunochemical procedures.

Robust, universal biomarker assay to detect senescent cells in biological specimens.

Cellular senescence contributes to organismal development, aging, and diverse pathologies, yet available assays to detect senescent cells remain unsatisfactory. Here, we designed and synthesized a lipophilic, biotin-linked Sudan Black B (SBB) analogue suitable for sensitive and specific, antibody-enhanced detection of lipofuscin-containing senescent cells in any biological material. This new hybrid histo-/immunochemical method is easy to perform, reliable, and universally applicable to assess senescence in biomedicine, from cancer research to gerontology.

Sudan Black B, The Specific Histochemical Stain for Lipofuscin: A Novel Method to Detect Senescent Cells.

The Sudan-Black-B (SBB) histochemical stain is well known to specifically react against lipofuscin, an aggregate of oxidized proteins, lipids, and metals. Lipofuscin is related to many ageing processes. It is also known to accumulate in senescent cells. We recently proved that lipofuscin detection, when applying the SBB staining, is highly specific for the visualization of senescent cells. Here, we present in detail this SBB method that can detect senescent cells in any material, irrespective of its preparation. This provides unique advantages not only in understanding physiological processes and the pathophysiology of various diseases but also in estimating the response to therapeutic interventions.