Label-free fluorescence aptasensor for the detection of cadmium(II) ion based on the conformational switching of aptamer and thioflavine T

A simple label-free Cd2+ fluorescent aptasensor was proposed using aptamer as a recognition element and thioflavine T (ThT) as a signal reporter. The presence of Cd(II) can induce the conformational switching of the aptamer probe, accompanied by a change in fluorescence intensity. According to the difference in fluorescence signals before and after the addition of Cd2+, a fluorescence sensor for Cd2+ assay was established. Under the better experimental conditions, the sensor displayed a good linear range from 2 to 50 nM and the excellent detection limit was 0.8 nM. The method demonstrated high sensitivity and good selectivity. The aptasensor could detect Cd2+ in simulated water samples with satisfactory results. The proposed method had obvious advantages that was without chemical modification of fluorescent groups and complicated target preconcentration. It provided a new analytical platform for the detection of heavy metal ion pollution in environmental and biomedical fields.

Fluorescent Properties of Cyanine Dyes As a Matter of the Environment

In non-viscous aqueous solutions, the cyanine fluorescent dyes Cy3 and Cy5 have rather low fluorescence efficiency (the fluorescence quantum yields of Cy3 and Cy5 are 0.04 and 0.3, respectively [1, 2]) and short excited state lifetimes due to their structural features. In this work, we investigated the effect of solubility and rotational degrees of freedom on the fluorescence efficiency of Cy3 and Cy5 in several ways. We compared the fluorescence efficiencies of two cyanine dyes sCy3 and sCy5 with the introduction of a sulfonyl substituent in the aromatic ring as well as covalently bound to T10 oligonucleotides. The results show that because of the different lengths of the polymethine chains between the aromatic rings of the dyes, cis-trans-isomerization has a much greater effect on the Cy3 molecule than on the Cy5 molecule, while the effect of aggregation is also significant.

A Simple Immunofluorescence Method to Characterize Neurodegeneration and Tyrosine Hydroxylase Reduction in Whole Brain of a Drosophila Model of Parkinson's Disease

Dopaminergic (DAergic) neurodegeneration in the substantia nigra pars compacta of the human brain is the pathological feature associated with Parkinson's disease (PD). Drosophila also exhibits mobility defects and diminished levels of brain dopamine on exposure to neurotoxicants mimicking PD. Our laboratory demonstrated in a Drosophila model of sporadic PD that there is no decrease in DAergic neuronal number; instead, there is a significant reduction in tyrosine hydroxylase (TH) fluorescence intensity (FI). Here, we present a sensitive assay based on the quantification of FI of the secondary antibody (ab). As the FI is directly proportional to the amount of TH synthesis, its reduction under PD conditions denotes the decrease in the TH synthesis, suggesting DAergic neuronal dysfunction. Therefore, FI quantification is a refined and sensitive method to understand the early stages of DAergic neurodegeneration. FI quantification is performed using the ZEN 2012 SP2 single-user software; a license must be acquired to utilize the imaging system to interactively control image acquisition, image processing, and analysis. This method will be of good use to biologists, as it can also be used with little modification to characterize the extent of degeneration and changes in the level of degeneration in response to drugs in different cell types. Unlike the expensive and cumbersome confocal microscopy, the present method will be an affordable option for fund-constrained neurobiology laboratories. Key features • Allows characterizing the incipient DAergic and other catecholaminergic neurodegeneration, even in the absence of loss of neuronal cell body. • Great alternative for the fund-constrained neurobiology laboratories in developing countries to utilize this method in different cell types and their response to drugs/nutraceuticals.

Harmonization of ANA testing challenge: quantification strategy to accurately predict end-point titers avoiding serial dilution

Despite the advantages of automated systems for antinuclear antibody (ANA) analysis, the prediction of end-point titers avoiding serial dilutions is still in progress. The aims of this study were to set a conversion table providing discriminant ranges of fluorescence signal intensity values (FI) corresponding to the end-point titers and validate this tool in a real-life laboratory setting. Eight hundred ninety-four serum samples were analyzed for ANA using Image Navigator System. In order to classify FI into non-overlapping groups corresponding to conventional end-point titers, statistical discriminant analysis was used. Validation study was performed calculating agreement and error rates between visual readings and conversion table of 1119 routine ANA positive samples. Setting of FI ranges corresponding to the end-point titers for different staining patterns was computed. For samples showing single pattern, the overall agreement between visual readings and conversion table was 98.4% for all titers ranging from 1:160 to 1:2560, of which 68.0% had the same titer and 30.4% were within ± one titer difference. Concordance rates according to ANA patterns were as follows: (1) nuclear 98.4%, of which 67.0% had the same titer and 31.4% ± one titer; (2) cytoplasmic 100%, of which 72.7% had the same titer and 27.3% than ± one titer; (3) mitotic 66.6%, of which 33.3% had more ± one titer. Our study developed a quantification method for autoantibodies titers assessment based on just one single sample dilution instead of traditional serial dilution approach, providing significant advantages in routine laboratory in terms of reduction in hand-on time and harmonization of results.

Immunofluorescence microscopy of G-quadruplexes and R-loops

A large variety of non-B secondary structures can be formed between DNA and RNA. In this chapter, we focus on G-quadruplexes (G4) and R-loops, which can have a close structural interplay. In recent years, increasing evidence pointed to the fact that they can strongly influence each other in vivo, both having physiological and pathological roles in normal and cancer cells. Here, we detail specific and accurate methods for purification of BG4 and S9.6 antibodies, and their subsequent use in immunofluorescence microscopy, enabling single-cell analysis of extent and localization of G4s and R-loops.

Temperature Effect on Fluorescence Intensity and Dipole Moment Using Thermochromic Shift Method of 7DA3MHBI-2HChromen-2-one Laser Dye in Highly Viscous Glycerol Solvent

The steady-state method is used to study the effect of temperature on the fluorescence characteristics of 7-(diethylamino)-3-(1-methyl-1H-benzo[d]imidazol-2-yl)-2H-chromen-2-one (7DA3MHBI-2HChromen-2-one) laser dye in glycerol solvent for the temperature range 293-343 K. Absorption and emission characteristics are affected by varying temperatures due to induced thermal effects. Transition probabilities mechanism of non-radiative and radiative are studied and frequency dependent parameters are estimated. Dipole moments in the ground and excited state are estimated using the thermochromic shift method over general solvatochromic methods.

Production and Purification of Cysteine-Rich Leptospiral Virulence-Modifying Proteins with or Without mCherry Fusion

Recombinant fluorescent fusion proteins are fundamental to advancing many aspects of protein science. Such proteins are typically used to enable the visualization of functional proteins in experimental systems, particularly cell biology. An important problem in biotechnology is the production of functional, soluble proteins. Here we report the use of mCherry-fusions of soluble, cysteine-rich, Leptospira-secreted exotoxins in the PF07598 gene family, the so-called virulence modifying (VM) proteins. The mCherry fusion proteins facilitated the visual detection of pink colonies of the VM proteins (LA3490 and LA1402) and following them through lysis and sequential chromatography steps. CD-spectroscopy analysis confirmed the stability and robustness of the mCherry-fusion protein, with a structure comparable to AlphaFold structural predictions. LA0591, a unique member of the PF07598 gene family that lacks N-terminal ricin B-like domains, was produced without mCherry tag that strengthens the recombinant protein production protocol without fusion protein as well. The current study provides the approaches for the synthesis of 50-125 kDa soluble, cysteine-rich, high-quality fast protein liquid chromatography (FPLC)-purified protein, with and without a mCherry tag. The use of mCherry-fusion proteins enables a streamlined, efficient process of protein production and qualitative and quantitative downstream analytical and functional studies. Approaches for troubleshooting and optimization were evaluated to overcome difficulties in recombinant protein expression and purification, demonstrating biotechnology utility in accelerating recombinant protein production.

Synthesis and performance analysis of zeolitic imidazolate frameworks for CO2 sensing applications

In this paper, we investigate the potential use of Zeolitic Imidazolate Frameworks (ZIF-8) as a sensing material for CO2 detection. Three synthesis techniques are considered for the preparation of ZIF-8, namely room temperature, microwave-assisted, and ball milling. The latter is a green and facile alternative for synthesis with its solvent-free, room-temperature operation. In addition, ball milling produces ZIF-8 samples with superior CO2 adsorption and detection characteristics, as concluded from fluorescence measurements. Characterization tests including X-ray diffraction (XRD), Fourier transform infrared (FTIR), Thermogravimetric analysis (TGA), Field emission scanning electron microscopy (FE-SEM) and Energy-dispersive X-ray spectroscopy (EDS) are conducted to inspect the structural morphology, the thermal stability, and elements content of the ZIF-8 samples obtained from the different aforementioned synthesis techniques. The characterization tests revealed the appearance of a new phase of ZIF-8 which is ZIF-L when deploying the ball milling technique with different structure, morphology, response to CO2 exposure and thermal stability when compared to its counterparts. Fluorescence measurements are carried out to evaluate the limit of detection (LOD), selectivity, and recyclability of the different ZIF-8 samples. The LOD of the ZIF-8 sample synthesized based on ball milling synthesis technique is 815.2 ppm, while LODs of the samples obtained from microwave and room temperature-based synthesis techniques are 1780.6 ppm and 723.8 ppm, respectively. This indicates that the room temperature and ball milling produced MOFs have comparable LODs. However, the room temperature procedure requires the use of a harmful solvent. The range of LOD demonstrates the suitable use of ZIF-8 for indoor air quality monitoring and other industrial applications.

Myeloprotection with activated carbon in doxorubicin-treated rats

Chemotherapy can often cause a variety of side effects including bone marrow (BM) suppression, termed as myelosuppression. Accordingly, facile and effective management of chemotherapy-induced myelosuppression is currently a pivotal task for experimental pathologists and oncologists. Here, we chose to use activated carbon (AC) with an extensive surface area for studying its possible protective effectiveness with respect to BM in doxorubicin (DOX)-treated rats. Spherical AC with an extended surface area up to 4490 m2/g was prepared for per os (p/o) delivery, whereas for intraperitoneal (i/p) delivery we used the powdered form of AC that was derived from the aforementioned spherical AC. During the monthly treatment of animals with AC and DOX these two components were delivered alternately (not in the same day). After treatment, BM cells were isolated from femurs of sacrificed animals, stained with acridine orange (AO) and analyzed by flow cytometry. Regardless of the route of AC delivery (p/o or i/p), apparent myeloprotection with a possible regenerative effect was observed in animals that received DOX, as evidenced by recovery of the populations of total nucleated cells (TNC) and polychromatic (immature) erythrocytes accompanied by a considerable reduction of the number of apoptotic/dead cells among TNC (≤2.0%). Moreover, as a result of AC administrations, there was a significant increase of AO green and far-red fluorescence intensities in the population of TNC, which is suggestive of the ongoing quantitative and conformational changes in DNA and RNA associated with cell recovery and proliferation. Thus, AC preparations under the present experimental conditions can effectively tackle DOX-induced myelosuppression via mechanisms not necessarily associated with adsorptive detoxification.

A fluorescent probe for detecting mitochondrial viscosity and its application in distinguishing human breast cancer cells from normal ones

Mitochondrial viscosity is closely associated with intracellular physiological activities yet their abnormality will result in various diseases. In particular, viscosity in cancer cells is different from that in normal cells, which is thought to be an indicator for cancer diagnosis. However, there were few fluorescent probes able to distinguish homologous cancer and normal cells by detecting mitochondrial viscosity. Herein, we designed a viscosity-sensitive fluorescent probe (named NP) based on the twisting intramolecular charge transfer (TICT) mechanism. NP exhibited exquisite sensitivity to viscosity and selectivity to mitochondria and excellent photophysical properties, such as large Stokes shift and high molar extinction coefficient, which enables wash-free, high-fidelity and fast imaging mitochondria. Moreover, it was capable of detecting mitochondrial viscosity in living cells and tissue, as well as monitoring apoptosis process. Significantly, considering numerous breast cancer cases in every country of the world, NP was successfully applied to distinguish human breast cancer cells (MCF-7) from normal cells (MCF-10A) by difference in fluorescence intensity originated from abnormality in mitochondrial viscosity. All the results indicated that NP could serve as a robust tool for effectively detecting mitochondrial viscosity changes in-situ.

The influence of storage conditions on fingermarks developed with 1,2-indanedione-ZnCl

The most important class of reagents for the enhancement of fingermarks on porous surfaces are those that react with the amino acid constituents of fingermarks. Ninhydrin, DFO (1,8-diazafluoren-9-one), and 1,2-indanedione are the three most common techniques widely known in forensic laboratories for the visualization of latent fingermarks on porous surfaces. In 2012 the Netherlands Forensic Institute replaced DFO by 1,2-indanedione-ZnCl after an internal validation, just like an increasing numbers of laboratories. In 2003, Gardner et al. published an article showing that fingermarks treated with 1,2-indanedione (without ZnCl), that were stored in daylight only decreased by 20% in fluorescence in 28 days. However, during casework we observed that the fluorescence of fingermarks treated with 1,2-indanedione with ZnCl decreased more rapidly. In this study, the effect of various storage conditions and aging times on the fluorescence of marks after treatment with 1,2-indanedione-ZnCl were assessed. Latent printed fingermarks from the digital matrix printer (DMP) and natural fingermarks from a known donor were used. The results showed that storing fingermarks in daylight (wrapped and un-wrapped) drastically decrease (over 60% loss) in fluorescence in approximately three weeks. Storage of the marks in a dark environment (at room temperature, in the refrigerator or even in the freezer) resulted in a decrease in fluorescence of less than 40%. Our recommendation is to always store treated fingermarks with 1,2-indanedione-ZnCl in a dark environment and, if possible, photographing them directly (within 1-2 days after treatment) to minimize the decrease of fluorescence.

Quantitative models and potential surrogates for rapid evaluation and surveillance of chlorine disinfection efficacy in reclaimed water

Chlorine disinfection has become the most widely applied and indispensable technology in wastewater treatment and reuse to mitigate microbial risk and guarantee water safety. However, owing to complexities and high concentrations of contaminants in reclaimed water, rapid evaluation of chlorine disinfection efficacy is a crucial but challenging issue. Based on intensive experimental and statistical analyses, this study has established kinetic models and potential surrogates for rapid indication of the inactivation of microbial indicators and opportunistic pathogens during chlorine disinfection in different reclaimed waters. Overall, the constructed Selleck models performed very well to simulate log removal values (LRVs) of fecal coliforms, Pseudomonas aeruginosa and heterotrophic plate counts in all reclaimed water samples (R² = 0.877-0.990). Moreover, total and Peak A fluorescence intensity as well as fluorescence integral intensities in Regions II and IV were found to have high response sensitivities during the chlorination process. Nevertheless, their effectiveness to act as potential surrogates of LRVs of microbial indicators needs to be further validated. The results from this study can provide valuable information on microbial safety surveillance of disinfection toward sustainable and long-term water reuse.

Preparation and pH Detection Performance of Rosin-Based Fluorescent Polyurethane Microspheres

Rosin-based fluorescent polyurethane emulsion (FPU) was prepared using isophorone diisocyanate, ester of acrylic rosin and glycidyl methacrylate, 1,5-dihydroxy naphthalene (1,5-DN), and 1,4-butanediol as the raw materials. Then, rosin-based fluorescent polyurethane microspheres (FPUMs) were successfully prepared by suspension polymerization method using FPU as the main material, azodiisobutyronitrile as the initiator, and gelatin as the dispersant. FPUMs were characterized by Fourier transform infrared spectra, thermogravimetric analysis, optical microscopy, scanning electron microscopy and fluorescence spectra, and the response performance of FPUMs to pH was studied. The results showed that FPUMs were successfully prepared. With the increase of the level of 1,5-DN, the particle size of FPUMs increased gradually, and the fluorescence intensity increased first and then decreased. When the level of 1,5-DN was 3 wt.%, the average particle size was 49.3 μm, the particle distribution index (PDI) was 1.05, and the fluorescence intensity was the largest (3662 a.u.). The fluorescence intensity of FPUMs increased linearly with the decrease of pH, which can be used for pH detection in solution. Furthermore, the FPUMs exhibited good thermal stability, anti-interference and recoverability.

Uptake and distribution of microplastics of different particle sizes in maize (Zea mays) seedling roots

Microplastics (MPs) pollution may be harmful to terrestrial ecosystems and is receiving increasing attention. A microcosm study on the uptake of MPs in maize (Zea mays) seedling roots exposed to small polystyrene (PS) beads (0.2, 0.5 and 1.0 μm) and large PS beads (2.0 and 5.0 μm) at 50 mg L^-1 for 7 d was performed. Additionally, the absorption ability of different parts of the roots was also investigated after 10 d of exposure with 0.2 μm PS beads. The results showed that root and shoot biomass remained unchanged under different particle sizes of PS beads. The small PS beads markedly increased the accumulation and distribution of PS beads in roots more than large ones. Confocal laser scanning micrographs confirmed that strong fluorescence signals from small PS beads (0.2 μm) were seen in all tissues, as compared with the control. Large PS beads (2.0 μm) were mainly distributed in the xylem, and no PS beads were detected in any root tissues when treated with 5.0 μm PS beads. More PS beads were absorbed by the root maturation zone than by the root tip zone. Fluorescence intensity values of PS bead accumulations measured across the tissues further confirmed these results. As seen in scanning electron microscopy images, small PS beads assembled on the cell wall of the xylem, while large PS beads (2.0 μm) were scattered on the cell walls of root xylem. The present study revealed the effects of different PS bead sizes on accumulation and distribution in maize roots, as well as the absorption ability of different positions of the roots. Moreover, fluorescence intensity could be a useful method to evaluate the uptake and distribution of MPs accurately.

Biomineralization-inspired magnetic nanoflowers for sensitive miRNA detection based on exonuclease-assisted target recycling amplification

Biomineralization-inspired magnetic hybrid nanoflowers were prepared facilely, and capture probes were easily immobilized on the obtained nanoflowers without tedious processing. Based on the magnetic hybrid nanoflowers and exonuclease-assisted target recycling amplification, a fluorescence miRNA sensor was fabricated. The presence of target miRNA leads to the formation of the double-strand structure, which would then be selectively digested by the exonuclease and increase fluorescence intensity. The target miRNA can be released for recycling and signal amplification. Under optimized reaction conditions, the hybrid nanoflower-based miRNA sensor had a broad detection range from 0.001 nM to 100 nM and a limit of detection of 0.23 pM (S/N = 3). The sensitive detection of miRNA in serum was also achieved with recoveries from 94.3% to 116.1%. This work provides a new insight into the fabrication of bioconjugated materials and shows great potential in miRNA sensing.

Exploratory application of indocyanine green quantification in biliary atresia observational study

BACKGROUND

Indocyanine green (ICG) is known to facilitate real-time imaging of the bile outflow during the Kasai procedure. This study explored more possibilities for applying ICG quantification in biliary atresia (BA).

METHODS

We enrolled nine BA patients in this study. All patients received intravenous ICG injections before surgery and underwent Kasai operation. With a fluorescence imaging system (Nanjing Nuoyuan, REAL-IGS FLI-108) to observe the ICG and quantify the ICG fluorescence intensity (ICG-FI) changes of the hepatic portal fibrous tissue and the liver during the operation. As a short-term prognosis assessment, we monitored the postoperative ICG metabolism time in stool and used the jaundice-free (TBIL < 2 mg/dl) at 1-3 months after the operation.

RESULTS

The average age of the patients at the time of surgery was 73 days. There were no adverse reactions after ICG injection. All patients were observed ICG-FI increased after the dissection of hepatic portal fibrous tissue, and the ICG-FI of the liver decreased during the operation. They all received standardized treatment after surgery. Four patients completely metabolized ICG within about two weeks (no fluorescence detected in stool), and the other five were longer than two weeks. Five patients achieved a jaundice-free outcome in the short-term postoperatively, and the other four did not.

CONCLUSIONS

It is feasible to quantify ICG-FI in real-time to evaluate the anatomical degree of hepatic portal fibrous tissue in BA. The variations of ICG-FI in the liver and postoperative ICG metabolism time may be related to prognosis.

Covalent organic framework-based fluorescent nanoprobe for intracellular pH sensing and imaging

Lysosomes are the acidic organelles in the cells that play an important role in intracellular degradation and other various cellular functions. The pH disturbance of lysosomes will result in the lysosomal dysfunction and many lysosomal related diseases. In this work, we reported a methoxy-based covalent organic framework (TAPB-DMTP-COF) that a novel pH-responsive fluorescent probe for lysosomal pH imaging in cells. The prepared TAPB-DMTP-COF presented regular crystal structure, low toxicity and good pH responsive property. The rich imine structure in the material enabled pH-responsive properties of the TAPB-DMTP-COF and made it exhibited pH-dependent fluorescence response. Good detection linearity for pH measurements in aqueous solution was achieved by this probe. Moreover, the TAPB-DMTP-COF can be used for the selective lysosomal pH imaging. Confocal fluorescence imaging results demonstrated that the pH fluctuations (from 4.0 to 7.4) and the pH changes in lysosomes can be effectively monitored in situ by the developed probe. This study may provide a new avenue for the intracellular pH sensing, deep study and understanding about the mechanism of diseases related to abnormal lysosomal pH.

Detection of small molecules by fluorescence intensity using single dye labeled aptamers and quencher transition metal ions

We describe herein an aptamer-based sensing approach that signal the presence of small-molecule targets when fluorescent DNA probes are challenged with the Ni²⁺ or Co²⁺ quencher metal ions. Functional oligonucleotides targeting L-tyrosinamide (L-Tym), adenosine (Ade) or cocaine (Coc) were end-labeled by the Texas-Red fluorophore. A fluorescence quenching occurred upon association of these transition metal ions with the free conjugates. The formation of the target-probe complex, by the way of variations in the overall binding of quencher metal ions along the DNA strands, led to a partial restoration (for the Ade and Coc systems) or a further attenuation (for the L-Tym system) of the fluorescence intensity. The absolute signal gain varied from 40 to 180% depending on the target-probe pair investigated. The approach was also used to detect the compound Ade in a spiked biological matrix in 1 min or less. The transition metal ion-based quenching strategy is characterized by its very simple implementation, low cost, and rapid signaling.

Electro-Modulation of Tubulin Properties and Function

Microtubules composed of tubulin heterodimers represent highly dynamic structures. These structures are essential for basic cellular functions, such as cell division. Microtubules can grow or shrink in response to environmental signals, principally chemical cues. Here, we provide an alternative-physical-strategy to modulate tubulin properties and its self-assembly process. The conformation and electrical properties of tubulin subunits are modulated by nanosecond electropulse signals. The formed structures of electrically treated tubulin are tightly linked to the degree of conformational and electrical properties changes induced by nanosecond electropulses. This strategy opens a new way for controlling the self-assembly process in biomolecules as well as in bioinspired materials.

Interaction of folate - Linked silica nanoparticles with HeLa cells: Analysis and investigation the effect of polymer length

This work is a continuance to our previous findings on silica nanoparticles (NPs) modified with diamine polymer, carboxymethyl-β-cyclodextrin (CM-β-CD) and folic acid (FA), respectively. When four different polymer lengths (D230, D400, D2000 and D4000) were analyzed, the release rate of anticancer agents was inversely related to the polymer length while the cell toxicity was directly related to the length. We investigate here the effect of polymer length on the extent of cellular interaction with HeLa cells. The mean particle size, the polydispersity (PD) and the zeta potential of the NPs were measured using dynamic light scattering (DLS), the quantitative analysis of the extent of NPs' interaction was studied using fluorescence microscopy and transmission electron microscopy (TEM) was used to qualitatively visualize them. The particle size increased by increasing the polymer length, the PD values were within the acceptable ranges (0.3−0.5) and the zeta potential was in the range of (−16 to −20 mV). A direct relation was observed between the fluorescence intensity and the length. All modified NPs were capable of entering the cells, however a greater number of NPs with long polymers was observed compared to short polymers. Thus, the direct relation of polymer length to the cell toxicity is due to the release rate behavior and the enhanced interaction of NPs which possess long polymers.

Genome-wide association analyses of carcass traits using copy number variants and raw intensity values of single nucleotide polymorphisms in cattle

BACKGROUND

The carcass value of cattle is a function of carcass weight and quality. Given the economic importance of carcass merit to producers, it is routinely included in beef breeding objectives. A detailed understanding of the genetic variants that contribute to carcass merit is useful to maximize the efficiency of breeding for improved carcass merit. The objectives of the present study were two-fold: firstly, to perform genome-wide association analyses of carcass weight, carcass conformation, and carcass fat using copy number variant (CNV) data in a population of 923 Holstein-Friesian, 945 Charolais, and 974 Limousin bulls; and secondly to perform separate association analyses of carcass traits on the same population of cattle using the Log R ratio (LRR) values of 712,555 single nucleotide polymorphisms (SNPs). The LRR value of a SNP is a measure of the signal intensity of the SNP generated during the genotyping process.

RESULTS

A total of 13,969, 3,954, and 2,805 detected CNVs were tested for association with the three carcass traits for the Holstein-Friesian, Charolais, and Limousin, respectively. The copy number of 16 CNVs and the LRR of 34 SNPs were associated with at least one of the three carcass traits in at least one of the three cattle breeds. With the exception of three SNPs, none of the quantitative trait loci detected in the CNV association analyses or the SNP LRR association analyses were also detected using traditional association analyses based on SNP allele counts. Many of the CNVs and SNPs associated with the carcass traits were located near genes related to the structure and function of the spliceosome and the ribosome; in particular, U6 which encodes a spliceosomal subunit and 5S rRNA which encodes a ribosomal subunit.

CONCLUSIONS

The present study demonstrates that CNV data and SNP LRR data can be used to detect genomic regions associated with carcass traits in cattle providing information on quantitative trait loci over and above those detected using just SNP allele counts, as is the approach typically employed in genome-wide association analyses.

Variations of disinfection byproduct precursors through conventional drinking water treatment processes and a real-time monitoring method

In this investigation, raw water (RW), settled water (SW), and filtered water (FW) collected from a drinking water treatment plant were fractionated into 24 natural organic matter (NOM) fractions with varying molecular weights and hydrophobicity. The yields of disinfection byproducts (DBPs) obtained during the chlorination of the NOM fractions were explored. Results revealed that the 0-1 kDa, 5-10 kDa, and hydrophobic DBP precursors dominated RW. Hydrophobic fractions cannot be effectively removed, which contributed to the high DBP precursors remaining in the FW. The optional optical parameters, including UVA (UV₃₄₀, UV₃₆₀, and UV₃₈₀), UVB (UV₂₈₀, UV₃₀₀, and UV₃₁₀), and UVC (UV₂₅₄, UV₂₆₀, and UV₂₇₂), were analyzed to determine the DBP yields during chlorination of different NOM fractions. Results revealed that UVC could be applied to indicate the regulated DBP yields of the humified precursors. Contrary to the generally accepted view, for biologically derived precursors, their regulated DBPs and dichloroacetonitrile correlated better with UVA (e.g. UV₃₄₀). Moreover, PARAFAC analysis was applied to decompose an array of 24 EEM spectra. Good linear correlations were found between the PARAFAC components and most DBP yields. Furthermore, four fluorescence parameters were proposed via a modified fluorescence picking method, which can serve as excellent surrogates of PARAFAC components. These fluorescence parameters were found to be effective in indicating most DBP yields. Finally, the fluorescence intensity at excitation wavelength/emission wavelength = 310/416 nm was found to be a promising built-in parameter for the real-time monitoring of DBP precursors, regardless of the humification degree of the precursors.

Analysis of decay kinetics of the cytosolic calcium transient induced by oxytocin in rat myometrium smooth muscle cells

The method of kinetic analysis of the relaxation phase of the mechanical response of the smooth muscle previously proposed by Burdyga and Kosterin was applied to study the dynamics of the decay of oxytocin-induced calcium transients in cytosol of the rat myometrium smooth muscle cell detected by a fluorescence signal generated by a calcium-sensitive probe fluo-4 using a laser scanning confocal microscope. The experimental data were well linearized in the coordinates ln [(F_m - F)/F] vs lnt (F and F_m are the current fluorescence intensity of the calcium probe and the fluorescence intensity at the maximum of the calcium transient, respectively, while t is the time). The empirical parameters n and τ were determined by which the maximal normalized relaxation rate V_n was calculated for five different ROIs (regions of interest) in the myocyte cytosol. It proved to be almost the same for all ROIs. The maximal normalized relaxation rate calculated from the fluorescence intensity was always lower than that calculated from the corresponding calcium concentration, i.e. the cytosolic Ca²⁺ concentration in the relaxation phase decreases faster than the corresponding fluorescence intensity. The value of the maximal normalized relaxation rate calculated both from the fluorescence intensity and from the force of oxytocin-induced contractions of isolated rat uterus longitudinal smooth muscles (according to Tsymbalyuk and Kosterin) was exactly the same. This indicates that in the relaxation phase, the decreasing curves of both the fluorescence intensity and the contraction forces coincide.

[Factors affecting the near-infrared autofluorescence intensity of parathyroid glands and intraoperative identification of parathyroid glands]

Objective: To evaluate the potential factors influencing the parathyroid autofluorescence intensity of near-infrared fluorescent (NIRF) and further value of NIRF in identifying the parathyroid during surgery. Methods: The clinical data of 51 patients who underwent thyroid or parathyroid surgery in the Department of Thyroid Surgery, the First Affiliated Hospital of Zhengzhou University from April to June 2019 were retrospectively analyzed, including 16 males and 35 females, aged 18 to 74 years.The fluorescence intensity (FI) of the parathyroid glands, thyroid glands and background, and the number of parathyroid glands detected by NIRF and white light were measured. Variance analysis, two independent samples t test and Spearman rank correlation analysis were used to analyze the relationship between standardized parathyroid FI and clinical variables. Chi square test was used to analyze the difference of parathyroid detection rate between NIRF and white light. Results: In the 51 patients, the mean standardized parathyroid FI was greater than the standardized thyroid FI (1.72 ± 0.68 vs. 1.25 ± 0.40, t=6.555, P<0.001). The standardized parathyroid FI was not associated with gender, age, operation type, BMI, preoperative serum Ca(2+), parathyroid hormone and calcitonin (all P>0.05), but it was associated with disease type (F=2.636, P<0.05). The mean standardized parathyroid FI of SHPT was lower than that of PTC, PTC with nodular goiter or NG(0.70±0.28 vs. 1.86±0.70, 1.69±0.49, 1.64±0.44, t value was 3.023, -1.129,-2.019, respectively, all P<0.05). There was no difference in the standardized parathyroid FI between SHPT and PHPT (1.34±0.18, t=1.218, P>0.05). There was no difference in standardized parathyroid FI between PHPT, PTC, NG, and PTC with NG(all P>0.05). Except for 3 cases of SHPT, 117 parathyroid glands were detected by NIRF and 101 parathyroid glands were detected by white light. The detection rate of parathyroid glands detected by NIRF was higher than that detected by white light (98.32% vs. 84.87%, χ(2)=13.974, P<0.001). In SHPT, the detection rate of parathyroid gland by NIRF was 25.00%. Conclusions: Except SHPT, parathyroid FI is not affected by other clinical variables. NIRF can improve the detection rate of parathyroid glands during operation.

Fluorescent Properties of Carboxyfluorescein Bifluorophores

Bright fluorescent probes with enhanced intensities in the fluorescein channel are of great value for plenty of biological applications. To design effective probes one should introduce as many as possible fluorophores to the biomolecule while leaving its native structure as intact as possible. To reach this compromise, we designed and synthesized fluorescein bifluorophores on the 3,5-diaminobenzoic acid scaffold, which allows for insertion of two fluorophores at one modification site of a biomolecule. Rigid structure of the branching linker group allows to minimize self-quenching the fluorophores. However, despite the structure similarities of fluorescein isomers (5-FAM and 6-FAM), different photophysical behavior was observed for the corresponding bifluorophores. Here we made efforts to get insight into these effects with the focus on the media viscosity impact.

Determination of Isoproturon in Environmental Samples using the QuEChERS Extraction-Spectrofluorimetric Method

An accurate and sensitive method has been developed for determination of the herbicide isoproturon using the Quick Easy Cheap Effective Rugged Safe (QuEChERS) extraction-spectrofluorimetric technique. The method involves the reaction of 2-cyanoacetamide with isoproturon in basic medium (NH₃ ; 15 mol/L). The resulting fluorescent product was found to show maximum emission at 378 nm and maximum excitation at 333 nm. Fluorescence intensity under the influence of different parameters was investigated. The linear range of analyte concentrations was found to be 0.5 to 15 µg/mL, with a limit of detection of 0.144 µg/mL, a limit of quantification of 0.437 µg/mL (signal to noise ratio = 3), and a regression coefficient of 0.9991, under optimized conditions. The proposed method was effectively applied for determination of isoproturon in different matrices; the percentage of recovery varied from 85.00 ± 1.2% to 96.00 ± 0.5%. The method was also applied for residue analysis of isoproturon in real soil samples collected from a pilot field. For extraction of isoproturon, the QuEChERS extraction approach was used, and the average residue in the soil samples was found to be 0.81 ± 0.07 µg/g. To show the potential of this approach, our results were compared with those of other methods reported in the literature. Environ Toxicol Chem 2019;38:2614-2620. © 2019 SETAC.

Immunoliposome-based fluorometric patulin assay by using immunomagnetic nanoparticles

A fluorometric immunoassay is described for the determination of patulin, a highly toxic fungal metabolite. A rabbit anti-patulin-bovine serum albumin (BSA) IgG conjugate was prepared and used to compose immunoliposomes and immunomagnetic nanoparticles. The immunomagnetic nanoparticles are then added to the sample to form the patulin-antibody composites which can be magnetically separated. The immunoliposomes are then added to form a sandwich. After magnetic separation of the composites and adding n-octyl-β-D-glucopyranoside, the fluorophore sulforhodamine B (SRB) is released. Its fluorescence intensity was then measured at excitation/emission wavelengths of 550/585 nm. The immunoliposome-based immunomagnetic nanoparticle assay can detect 8 μg L⁻¹ of patulin in apple juice without the need for extraction, separation, and purification. The detection limit falls within the European regulatory limit for infants and children’s products (10 μg L⁻¹). The method is rapid, enviroment-friendly, and reliable.

Graphical abstract

Structure and Fluorescence Intensity Measurements in Biofilms

Confocal laser scanning microscopy (CLSM) is one of the most relevant technologies for studying biofilms in situ. Several tools have been developed to investigate and quantify the architecture of biofilms. However, an approach to accurately quantify the intensity of a fluorescent signal over biofilm depth is still lacking. Here we present a tool developed in the ImageJ open-source software that can be used to extract both structure and fluorescence intensity from CLSM data: BIAM (Biofilm Intensity and Architecture Measurement). This is of utmost significance when studying the fundamental mechanisms of biofilm development, differentiation, and in situ gene expression or when aiming to understand the effect of external molecules on biofilm phenotypes.

How to Design Donor-Acceptor Based Heterocyclic Conjugated Polymers for Applications from Organic Electronics to Sensors

Over the past few years, significant progress has been made in the design of organic semi-conducting conjugated polymers that readily transport holes or electrons and can result in light emission. The conjugated backbone consist mainly of electron-donating (donor) and electron-withdrawing (acceptor) units as alternating groups in a conjugated oligomer or polymer that can be regulated by physical properties such as π conjugation length, monomer alteration, inter/intramolecular interactions and energy levels. Certainly, it is notable today that the highest occupied molecular orbital level of the producing material is localized predominantly on the electron-donating moiety and lowest unoccupied molecular orbital level on the electron-accepting moiety. Conjugated oligomers or polymers are used in many detecting fields due to their exceptional ability to sense toxic chemicals, metal ions and biomolecules. The conjugated polymers have unique delocalized π-electronic "molecular wires" that can expand the fluorescence intensity considerably. The fluorescence intensity of polymers can be quenched by particular quenching molecules. In this review, the fluorescence intensity, detecting of multiple metal ions, solubility, photochemical stability and optoelectronic properties of these conjugated polymers, and how they can be regulated by different functional groups, are discussed in detail.

Egg autofluorescence and options for detecting peanut agglutinin binding for the identification of Haemonchus contortus eggs in fecal samples

Quantifying eggs from Haemonchus and other trichostrongyle genera in sheep and goat fecal samples is important for evaluating control and treatment strategies for this family of nematodes with divergent pathologies, capabilities for anthelmintic resistance and environmental susceptibilities. Unfortunately, egg morphology among most of the genera do not differ enough to support the accurate identification of these genera with standard microscopic techniques. Several studies have identified specific lectins which bind selectively to sugars located on the egg surfaces for individual genera among the trichostrongyles. To detect lectins binding to these eggs, they must be directly or indirectly bound to fluorophores, and observed with an epi-fluorescence microscope. The binding of multiple lectins to isolated eggs from a fecal sample can be simultaneously detected if fluorophores are used whose excitation and emission spectra do not overlap, and this would enable the development of a fluorescence-based diagnostic test that identifies multiple trichostrongyle genera within each sample. The present study compared the usefulness of different, commercially available detection systems for use in detecting lectin binding to trichostrongyle eggs. Comparisons were made using the detection of PNA binding to H. contortus eggs with the goal of finding three systems with color spectra that do not overlap. These evaluations included both fluorophores directly conjugated to PNA in a one-step incubation protocol and a two-step incubation protocol involving biotinylated PNA and streptavidin conjugated to different fluorophores. Autofluorescence can affect the efficiency of any fluorescence-based detection system, and significant autofluorescence was observed among the unstained H. contortus eggs with the DAPI-type fluorescence filter, but it was significantly lower with the FITC-type filter and was virtually absent with the rhodamine-type filter. This study demonstrated that all the PNA detection methods tested with H. contortus eggs generated fluorescence intensities (FIs) that were significantly above the autofluorescence generated by the eggs among the three different fluorescence filters. Fluorescence intensities from PNA directly conjugated to either the FITC or rhodamine fluorophores were not different, but the lower autofluoresence in the rhodamine-type filter will enable this fluorophore to be detected more efficiently. Use of biotinylated PNA combined with streptavidin-conjugated to synthetic fluorophores (Alexa Fluor 405, 488 and 546) significantly increased FIs over that of the directly conjugated PNA, but there were no significant differences in FIs among these three biotin-avidin conjugation fluorophores. This biotin-avidin system required two incubation steps. Doubling the concentration of PNA also provided increased FI, at least for the biotin-avidin system. Adding an additional amplification step to the biotin-avidin system involving biotinylated anti-streptavidin followed by the streptavidin-Alexa Fluor complex also provided additional fluorescence.

Bright spot analysis for photodynamic diagnosis of brain tumors using confocal microscopy

BACKGROUND

In a previous study of photodynamic tumor diagnosis using 5-aminolevulinic acid (5-ALA), the authors proposed using fluorescence intensity and bright spot analyses under confocal microscopy for the precise discrimination of tumorous brain tissue (such as glioblastoma, GBM) from normal tissue. However, it remains unclear if bright spot analysis can discriminate infiltrating tumor in the boundary zone and whether this method is suitable for GBM with no 5-ALA fluorescence or for other tumor types.

METHODS

Brain tumor tissue resected from 5-ALA-treated patients was sectioned to evaluate bright spots under confocal microscopy with a 544.5 - 619.5 nm band-pass filter, which eliminated the fluorescence induced by 5-ALA. Border regions and adjacent normal tissues were observed for differences in bright spot distribution. Histopathology was also conducted by hematoxylin and eosin (H&E) staining of serial slices from the same samples to confirm the locations of tumorous, infiltrating, and normal regions. Bright spot areas were then calculated for the same regions evaluated by histopathology. This method was applied for GBM with and without 5-ALA-induced fluorescence as well as for lower-grade gliomas and other brain tumor types.

RESULTS

The bright spot area was substantially smaller in the GBM body than in normal brain tissues. Bright spot area was also smaller in infiltrating tumors than in normal tissue at the margin. The same bright spot pattern was observed in tumorous tissues with no 5-ALA-induced fluorescence and in non-GBM tumors. The bright spot fluorescence is suggested to arise from lipofuscin based on emission spectra (mainly within 544.5 - 619.5 nm) and optimum excitation wavelength (about 405 nm).

CONCLUSIONS

Bright spot analysis is useful for discriminating infiltrating tumor from bordering normal tissue as an alternative or complement to photodynamic diagnosis with 5-ALA. This method is also potentially useful for tumors with no 5-ALA-derived red fluorescence and other nervous system tumors.

A fluorescence-based assessment of the fate of organic matter in water treated using crude/purified Hibiscus seeds as coagulant in drinking water treatment

This study used fluorescence excitation-emission matrices (EEMs) analysis to investigate the characteristics of natural organic matter (NOM) in treated water using okra crude extract (OCE), sabdariffa crude extract (SCE) and kenaf crude extract (KCE) as coagulants. In addition, an assessment of the impact of purified okra protein (POP), purified sabdariffa protein (PSP) and purified kenaf protein (PKP) was undertaken. The performance evaluation of these coagulants in terms of increase or decrease in dissolved organic carbon (DOC) was compared with Peak T fluorescence intensity observed at excitation wavelength 220-230 nm, and emission wavelength 340-360 nm. Fluorescence analysis of water treated with the crude extracts identified the removal of DOC in peaks A and C region whereas the increase in DOC from the protein was predominantly found in peaks T and B region. Furthermore, it was observed that the purified proteins were noted to be capable of reducing the DOC concentration in raw water where all fluorophores were not detected. The application of OCE, SCE and KCE yielded an increase in DOC of 65, 61 and 55% respectively, corresponding to increases of 65, 29 and 54% in peak T fluorescence intensities, at 100 mg/l dose. Furthermore, DOC concentration was reduced by 25, 24 and 18% using POP, PSP and PKP respectively as coagulants with corresponding decreases in fluorescence intensity of 46%, 44 and 36% in POP, PSP and PKP, at a lower dose of 0.1 mg/l. Therefore, it is clear that Peak T fluorescence intensity could be used to characterise organic matter in treated water using natural extracts to assess final water quality.

Tear dynamics under scleral lenses

PURPOSE

To evaluate post-lens tear dynamics at two different time points during scleral lens wear in two cohorts with 10 neophytes each.

METHODS

All subjects wore bilaterally scleral lenses for 5 h on 3 separate visits. Post-lens tear exchange was measured using Out-in method, which required 5 μL of 2% FITC-Dextran instilled on the bulbar conjunctiva during lens wear. Time taken to observe the first sign of fluorescence in post-lens tear reservoir was recorded with a stopwatch. Out-in measurements were collected at 5-hour  post-lens insertion in Group 1 and compared with those obtained at 20 min of lens wear in Group 2. Tear dynamics under the lens was observed in Group 2 with fluorogram using a modified slit-lamp technique (Tan et al., 2018) to monitor post-lens fluorescence intensity and with high-resolution spectral domain optical coherence tomography (ENVISU 2300; Bioptigen Inc.) to measure post-lens tear thickness (PoLTT) over 5 h of lens wear.

RESULTS

60% of subjects in Group 1 achieved Out-in times less than 5 min at 5-hour post-lens insertion, compared with 67% of subjects at 20-min lens wear (Tan et al., 2018). Using qualitative analysis on 60 series of data in Group 2 to compare the changes in fluorescence intensity and PoLTT with respect to lens-wearing time, 27% was due to lens settling, 13% was due to tear exchange and mixing while 60% indicated tear dynamics under scleral lenses was due to a combination of tear exchange, mixing, and lens settling.

CONCLUSION

Tear flow into tear reservoir under a scleral lens on subjects with healthy cornea occurred at 20 min and 5 h after lens insertion. After 5 h of lens wear, roughly one third of the subjects had no tear flow into post-lens reservoir, as the observed decline in post-lens tear fluorescence was predominately due to lens settling.

A methodology for detecting the wound state sensing in terms of its colonization of pathogenic bacteria

A methodology for wound state sensing in terms of its colonization with pathogenic bacteria such as Staphylococcus aureus or Pseudomonas aeruginosa has been developed. Here we report polydiacetylene (PDA) liposomes containing self-quenched carboxyfluorescein dye are only sensitive to toxins/enzymes secreted by Pathogenic bacteria but not by non-pathogenic species of Escherichia coli (DH5α). The basis of the detection assay is that at high concentration, carboxyfluorescein is non-fluorescent. Following breakdown of the bilayer of liposome containers by bacterial toxins, the dye becomes diluted and “switches on”. The methodology can be easily adapted to evaluate the release of payloads from PDA liposomes in terms of fluorescence intensity and in addition to detect the potential interaction mechanism of biomimetic bilayer and pathogenic bacteria.

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Self-quenched when encapsulated at high concentration, while fluorescence when diluted in solution

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Easy quantification by measuring fluorescence intensity

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Simple measurement procedure required (plate reading fluorimeter)

Quantitative assessment of fluorescence intensity of ICG in sentinel nodes in early gastric cancer

BACKGROUND

The sentinel node (SN) detection by dual tracer method using indocyanine green (ICG) and a radioisotope (RI) has been recommended for early gastric cancer. However, institutions are limited due to radioactivity in the RI method. The greatest advantage of the RI method is that it objectively assesses RI uptake as a numerical value. The aim of the present study was to verify the usefulness of ICG fluorescence intensity in SN.

METHODS

Seventeen patients with early gastric cancer were enrolled in this study. RI uptake by each lymph node was measured using Navigator GPS and fluorescence nodes were identified using the hyper eye medical system (HEMS). Fluorescence intensity in fluorescence nodes was evaluated using ICG intensity imaging software (Mizuho, Japan) of the HEMS.

RESULTS

The total number of dissected lymph nodes was 227, with an average of 13.3 per patient. The numbers of HN, FN-S, and FN-B were 64, 77, and 34. RI uptake was significantly greater by FN-S than by non-FN-S (P = 0.0016). The median fluorescence intensity value was higher in HN than in non-HN (P < 0.001). A correlation was observed between RI uptake and fluorescence intensity. Dissecting FNs with fluorescence intensity levels of 1-6 resulted in 92.1% dissection of HNs.

CONCLUSION

It is possible that the evaluation of fluorescence intensity is useful for selected SNs instead of RI tracer. If fluorescence intensity is measurable in surgery, an infrared fluorescence method using ICG may be useful and safe for the detection of SN in early gastric cancer.

Comparison of six digestion methods on fluorescent intensity and morphology of the fluorescent polystyrene beads

Effect of digestion methods on fluorescence intensity of fluorescent polystyrene (PS) beads was poorly understood, which may affect the accuracy of toxicity test of the fluorescent PS beads exposed to marine organisms. Therefore, six digestion approaches were compared on fluorescence intensities and properties of three commercial fluorescent PS beads. Among all the protocols, the digestion using KOH (10% w/v, 60 °C) (KOH-digestion) had no effect on the fluorescence intensity, morphology and composition of the three fluorescent PS beads. Moreover, the extraction efficiency ≥ 95.3 ± 0.2% of fluorescent PS beads in Daphnia magna and zebrafish, confirming its feasibility in fluorescent PS beads quantitative analysis. However, the fluorescence intensities of fluorescent PS beads digested by other five protocols were significantly decreased, as well as the change of morphology and composition on fluorescent PS beads. Overall, the KOH-digestion is an optimal protocol for extracting fluorescent PS beads in biological samples.

Optimizing the image of fluorescence cholangiography using ICG: a systematic review and ex vivo experiments

Background

Though often only briefly described in the literature, there are clearly factors that have an influence on the fluorescence intensity, and thereby the usefulness of the technique. This article aims to provide an overview of the factors influencing the fluorescence intensity of fluorescence imaging with Indocyanine green, primarily focussed on NIRF guided cholangiography.

Methods

A systematic search was conducted to gain an overview of currently used methods in NIRF imaging in laparoscopic cholecystectomies. Relevant literature was searched to gain advice on what methods to use. Ex vivo experiments were performed to assess various factors that influence fluorescence intensity and whether the found clinical advices can be confirmed.

Results

ICG is currently the most widely applied fluorescent dye. Optimal ICG concentration lies between 0.00195 and 0.025 mg/ml, and this dose should be given as early as achievable—but maximum 24 h—before surgery. When holding the laparoscope closer and perpendicular to the dye, the signal is most intense. In patients with a higher BMI and/or cholecystitis, fluorescence intensity is lower, but NIRF seems to be more helpful. There are differences between various marketed fluorescence systems. Also, no uniform method to assess fluorescence intensity is available yet.

Conclusions

This study identified and discussed several factors that influence the signal of fluorescence cholangiography. These factors should be taken into account when using NIRF cholangiography. Also, surgeons should be aware of new dyes and clinical systems, in order to benefit most from the potential of NIRF imaging.

Electronic supplementary material

The online version of this article (10.1007/s00464-018-6233-x) contains supplementary material, which is available to authorized users.

Rapid optimization of spore production from Bacillus amyloliquefaciens in submerged cultures based on dipicolinic acid fluorimetry assay

Some optimization techniques have been widely applied for spore fermentation based on the plate counting. This study optimized the culture medium for the spore production of Bacillus amyloliquefaciens BS-20 and investigated the feasibility of using a dipicolonic acid (DPA) fluorimetry assay as a simpler alternative to plate counting for evaluating spore yields. Through the single-factor experiment, the metal ions and agro-industrial raw materials that significantly enhanced spore production were determined. After conducting a response surface methodology (RSM) analysis of several metal ions, the combined use of optimum concentrations of Mn2+, Fe2+, and Ca2+ in culture media produced a 3.4-fold increase in spore yields. Subsequently, supplementing soybean meal and corn meal with optimum concentrations determined by another RSM analysis produced an 8.8-fold increase. The final spore concentration from a culture medium incorporating optimum concentrations of the metal ions and raw materials mentioned above was verified to reach (8.05 ± 0.70) × 109 CFU/mL by both DPA fluorimetry and plate counting. The results suggest that the use of DPA fluorescence intensity as an alternative value to colony counting provides a general method for assessing spore yields with less work and shorter time.

A comparative study of the spectral, fluorometric properties and photostability of natural curcumin, iron- and boron- complexed curcumin

Curcumin is a yellow phenolic compound with a wide range of reported biological effects. However, two main obstacles hinder the use of curcumin therapeutically, namely its poor bioavailability and photostability. We have synthesized two curcumin complexes, the first a boron curcumin complex (B-Cur₂) and the second an iron (Fe-Cur₃) complex of curcumin. Both derivatives showed high fluorescence efficiency (quantum yield) and greater photostability in solution. The improved photostability could be attributed to the coordination structures and the removal of β-diketone group from curcumin. The fluorescence and ultra violet/visible absorption spectra of curcumin, B-Cur₂ and Fe-Cur₃ all have a similar spectral pattern when dissolved in the same organic solvent. However, a shift towards a lower wavelength was observed when moving from polar to non-polar solvents, possibly due to differences in solvent polarity. A plot of Stokes' shift vs the orientation polarity parameter (Δf) or vs the solvent polarity parameter (E_T 30) showed an improved correlation between the solvent polarity parameter than with the orientation polarity parameter and indicating that the red shift observed could be due to hydrogen-bonding between the solvent molecules. A similar association was obtained when Stokes' shift was replaced by maximum synchronous fluorescence. Both B-Cur₂ and Fe-Cur₃ had larger quantum yields than curcumin, suggesting they may be good candidates for medical imaging and in vitro studies.

Understanding the fundamental mechanisms of biofilms development and dispersal: BIAM (Biofilm Intensity and Architecture Measurement), a new tool for studying biofilms as a function of their architecture and fluorescence intensity

Confocal laser scanning microscopy (CLSM) is one of the most relevant technologies for studying biofilms in situ. Several tools have been developed to investigate and quantify the architecture of biofilms. However, an approach to quantify correctly the evolution of intensity of a fluorescent signal as a function of the structural parameters of a biofilm is still lacking. Here we present a tool developed in the ImageJ open source software that can be used to extract both structural and fluorescence intensity from CLSM data: BIAM (Biofilm Intensity and Architecture Measurement). This is of utmost significance when studying the fundamental mechanisms of biofilm growth, differentiation and development or when aiming to understand the effect of external molecules on biofilm phenotypes. In order to provide an example of the potential of such a tool in this study we focused on biofilm dispersion. cis-2-Decenoic acid (CDA) is a molecule known to induce biofilm dispersion of multiple bacterial species. The mechanisms by which CDA induces dispersion are still poorly understood. To investigate the effects of CDA on biofilms, we used a reporter strain of Escherichia coli (E. coli) that expresses the GFPmut2 protein under control of the rrnBP1 promoter. Experiments were done in flow cells and image acquisition was made with CLSM. Analysis carried out using the new tool, BIAM, indicates that CDA affects the fluorescence intensity of the biofilm structures as well as biofilm architectures. Indeed, our results demonstrate that CDA removes more than 35% of biofilm biovolume and suggest that it results in an increase of the biofilm's mean fluorescence intensity (MFI) by more than 26% compared to the control biofilm in the absence of CDA.

Synthesis and fluorescence properties of six fluorescein-nitroxide radical hybrid-compounds

Six fluorescein-nitroxide radical hybrid-compounds (2ab, 3ab, 4, and 5) were synthesized by the condensation of 5- or 6-carboxy-fluorescein and 4-amino-TEMPO (2ab), 5- or 6-aminofluorescein and 4-carboxy-TEMPO (3ab), and fluorescein and 4-carboxy-TEMPO (4), or by reaction of the 3-hydroxyl group of fluorescein with DPROXYL-3-ylmethyl methanesulfonate (5). Fluorescence intensities (around 520nm) after reduction of the radical increased to 1.43-, 1.38-, and 1.61-folds for 2a, 2b and 3b respectively; 3a alone exhibited a decrease in intensity on reduction. Since 4 was readily solvolyzed in PBS or even methanol to afford fluorescein and 4-carboxy-TEMPO, its fluorescence change could not be measured. Hybrid compound 5 containing an ether-linkage between the fluorescein phenol and 3-hydroxymethyl-DPROXYL hydroxyl centers, was stable and on reduction, showed a maximum increase (3.21-fold) in relative fluorescence intensity in PBS (pH5.0), despite its remarkably low absolute fluorescence intensity.

Fluorescence intensity and bright spot analyses using a confocal microscope for photodynamic diagnosis of brain tumors

BACKGROUND

In photodynamic diagnosis using 5-aminolevulinic acid (5-ALA), discrimination between the tumor and normal tissue is very important for a precise resection. However, it is difficult to distinguish between infiltrating tumor and normal regions in the boundary area. In this study, fluorescent intensity and bright spot analyses using a confocal microscope is proposed for the precise discrimination between infiltrating tumor and normal regions.

METHODS

From the 5-ALA-resected brain tumor tissue, the red fluorescent and marginal regions were sliced for observation under a confocal microscope. Hematoxylin and eosin (H&E) staining were performed on serial slices of the same tissue. According to the pathological inspection of the H&E slides, the tumor and infiltrating and normal regions on confocal microscopy images were investigated. From the fluorescent intensity of the image pixels, a histogram of pixel number with the same fluorescent intensity was obtained. The fluorescent bright spot sizes and total number were compared between the marginal and normal regions.

RESULTS

The fluorescence intensity distribution and average intensity in the tumor were different from those in the normal region. The probability of a difference from the dark enhanced the difference between the tumor and the normal region. The bright spot size and number in the infiltrating tumor were different from those in the normal region.

CONCLUSIONS

Fluorescence intensity analysis is useful to distinguish a tumor region, and a bright spot analysis is useful to distinguish between infiltrating tumor and normal regions. These methods will be important for the precise resection or photodynamic therapy of brain tumors.

Rapid induction of GFP expression by the nitrate reductase promoter in the diatom Phaeodactylum tricornutum

An essential prerequisite for a controlled transgene expression is the choice of a suitable promoter. In the model diatom Phaeodactylum tricornutum, the most commonly used promoters for trans-gene expression are the light dependent lhcf1 promoters (derived from two endogenous genes encoding fucoxanthin chlorophyll a/c binding proteins) and the nitrate dependent nr promoter (derived from the endogenous nitrate reductase gene). In this study, we investigated the time dependent expression of the green fluorescent protein (GFP) reporter under control of the nitrate reductase promoter in independently genetically transformed P. tricornutum cell lines following induction of expression by change of the nitrogen source in the medium via flow cytometry, microscopy and western blotting. In all investigated cell lines, GFP fluorescence started to increase 1 h after change of the medium, the fastest increase rates were observed between 2 and 3 h. Fluorescence continued to increase slightly for up to 7 h even after transfer of the cells to ammonium medium. The subsequent decrease of GFP fluorescence was much slower than the increase, probably due to the stability of GFP. The investigation of several cell lines transformed with nr based constructs revealed that, also in the absence of nitrate, the promoter may show residual activity. Furthermore, we observed a strong variation of gene expression between independent cell lines, emphasising the importance of a thorough characterisation of genetically modified cell lines and their individual expression patterns.

An integrated analysis tool for analyzing hybridization intensities and genotypes using new-generation population-optimized human arrays

BACKGROUND

Affymetrix Axiom single nucleotide polymorphism (SNP) arrays provide a cost-effective, high-density, and high-throughput genotyping solution for population-optimized analyses. However, no public software is available for the integrated genomic analysis of hybridization intensities and genotypes for this new-generation population-optimized genotyping platform.

RESULTS

A set of statistical methods was developed for an integrated analysis of allele frequency (AF), allelic imbalance (AI), loss of heterozygosity (LOH), long contiguous stretch of homozygosity (LCSH), and copy number variation or alteration (CNV/CNA) on the basis of SNP probe hybridization intensities and genotypes. This study analyzed 3,236 samples that were genotyped using different SNP platforms. The proposed AF adjustment method considerably increased the accuracy of AF estimation. The proposed quick circular binary segmentation algorithm for segmenting copy number reduced the computation time of the original segmentation method by 30-67 %. The proposed CNV/CNA detection, which integrates AI and LOH/LCSH detection, had a promising true positive rate and well-controlled false positive rate in simulation studies. Moreover, our real-time quantitative polymerase chain reaction experiments successfully validated the CNVs/CNAs that were identified in the Axiom data analyses using the proposed methods; some of the validated CNVs/CNAs were not detected in the Affymetrix Array 6.0 data analysis using the Affymetrix Genotyping Console. All the analysis functions are packaged into the ALICE (AF/LOH/LCSH/AI/CNV/CNA Enterprise) software.

CONCLUSIONS

ALICE and the used genomic reference databases, which can be downloaded from http://hcyang.stat.sinica.edu.tw/software/ALICE.html , are useful resources for analyzing genomic data from the Axiom and other SNP arrays.

A novel Ag⁺ cation sensor based on polyamidoamine dendrimer modified with 1,8-naphthalimide derivatives

In this study, 4-amino-1,8-naphthalimide-conjugated polyamidoamine dendrimer was synthesized and characterized and its potentiality as a cation sensor was investigated. 4-Amino-1,8-naphthalic anhydride reacted with polyamidoamine dendrimer and the product was characterized using FTIR, (1)H NMR, (13)C NMR and melting point analysis method. The synthesized compound was applied to detect various cations in water media and N,N-dimethylformamide (DMF) via monitoring the quenching of the fluorescence intensity. Furthermore, various metal cations including Cu(2+), Ni(2+), Zn(2+), Pb(2+),Ca(2+), Ba(2+), Cd(2+), Hg(2+), Fe(2+), Fe(3+) and Ag(+) were tested. The complexes formed between the synthesized compound and metal cations in solution and their effects on Photoinduced Electron Transfer (PET) process were investigated regarding the potential application of the newly-synthesized dendrimer as a colorimetric and fluorescent sensor for such cations. The results clearly confirmed that the 1,8-naphthalimide groups surrounding the central dendrimer core showed strong green fluorescence emission at 553 nm. This effect considerably decreased with the introduction of all cations, except Ag(+) where the fluorescence quenching effect was remarkable and more dominant. Therefore, it can be concluded that the synthesized dye has the potentiality of being a highly sensitive and selective fluorescence sensor for Ag(+) cation.

A dark-to-bright reporter cell for classical swine fever virus infection

Current methods to quantitate classical swine fever virus (CSFV) infectivity in cell culture are time-consuming and labor-intensive. This study described the generation of a dark-to-bright fluorescent reporter cells to facilitate in vitro studies of CSFV infection and replication. This assay was based on a novel reporter cell stably expressing the enhanced green fluorescent protein (EGFP) fused in-frame to a quenching peptide via a special recognition sequence of the CSFV NS3 protease. Chromophore maturation of EGFP can be prevented by quenching peptide until the quenching peptide was specifically cleaved by NS3 protease during CSFV infection, making it a dark-to-bright reporter of CSFV infection. The result demonstrated that the CSFV-infected cells were clearly distinguishable from mock-infected cells and cells infected with other viruses. There was a strong correlation between the fluorescence intensity and viral RNA replication in CSFV-infected cells. The cell enabled rapid and sensitive detection of CSFV infection and viral replication in cell culture. The best time to examine the fluorescence in CSFV-infected cells was at 48h post-inoculation. These data suggested that the cells can be used as a reporter cell in CSFV infection assays. This reporter cell provides a sensitive method for the detection and isolation of CSFV and it will be useful for the screening of antiviral drugs or neutralizing antibody assays.

The joint effects of room temperature ionic liquids and ordered media on fluorescence characteristics of estrogens in water and methanol

This study investigated the steady-state and time-resolved fluorescence properties of 17α-ethinylestradiol (EE2) and 17β-estradiol (E2) in the presence of ordered media (β-cyclodextrins (β-CD) and cetyltrimethylammonium bromide (CTAB)). In addition, we analyzed the effects of four room temperature ionic liquids (RTILs) on the fluorescence intensities (FIs) of EE2/β-CD and E2/β-CD inclusion complexes in methanol. Both β-CD and CTAB enhanced the fluorescence of EE2 and E2. The FIs of EE2 and E2 with β-CD or CTAB in methanol were greater than those in water, possibly resulting from decreased oxygen-quenching in H2O molecules. β-CD and CTAB may form inclusion complexes with estrogen in both water and methanol. The inclusion ratio of the complex was 1:1 and the inclusion constant (K) values in water were greater than those in methanol. The fluorescence lifetimes were 2.50 and 4.13 ns for EE2 and 2.58 and 4.03 ns for E2 in aqueous solution and methanol, respectively. The changing trend of fluorescence lifetimes for EE2 and E2 in β-CD or CTAB was similar to the steady-state FIs. The four RTILs had a significant quenching effect on the FIs of EE2/β-CD and E2/β-CD, and the quenching process for EE2/β-CD and E2/β-CD by RTILs was demonstrated to be a dynamic quenching mechanism. Fluorescent data obtained from these complex systems provide a theoretical foundation for understanding the interaction mechanisms between ordered media and RTILs in the analysis of estrogens.

Molecular cloning and expression analysis of a new bilin lyase: the cpcT gene encoding a bilin lyase responsible for attachment of phycocyanobilin to Cys-153 on the β-subunit of phycocyanin in Arthrospira platensis FACHB314

To study the assembly of phycocyanin β subunit, the gene cpcT was first cloned from Arthrospira platensis FACHB314. To explore the function of cpcT, the DNA of phycocyanin β subunit and cpcT were transformed into Escherichia coli BL21 with the plasmid pET-hox1-pcyA, which contained the genes hemeoxygenase 1 (Hox1) and ferredoxin oxidoreductase (PcyA) needed to produce phycocyanobilin. The transformed strains showed specific phycocyanin fluorescence, and the fluorescence intensity was stronger than the strains with only phycocyanin β subunit, indicating that CpcT can promote the assembly of phycocyanin to generate fluorescence. To study the possible binding sites of apo-phycocyanin and phycocyanobilin, the Cys-82 and Cys-153 of the β subunit were individually mutated, giving two kinds of mutants. The results show that Cys-153 maybe the active site for β subunit binding to phycocyanobilins, which is catalyzed by CpcT in A. platensis FACHB314.

Elongated oligonucleotide-linked immunosorbent assay for sensitive detection of a biomarker in a microwell plate-based platform

The immunoassay is a representative method for detecting disease biomarkers and pathogenic biological agents. While the conventional enzyme-linked immunosorbent assay (ELISA) has been routinely used for the analysis of biological samples, methods with higher sensitivity are still in demand because the detection of low-level biomarkers is important for early diagnosis of lethal diseases. In this study, we developed a sensitive immunoassay called elongated oligonucleotide-linked immunoassay (EOLISA), employing long DNA oligonucleotides (80-mer), a fluorogenic RNA probe and RNase H for signal amplification. The elongated DNA oligonucleotides led to a highly amplified fluorescence signal via iterative cycles of DNA-RNA duplexation and subsequent degradation of the RNA in the duplex by RNase H. The immunoassay was evaluated for sensitive detection of fatty acid binding protein (FABP) in the 0-1 ng mL(-1) range. When compared with ELISA, EOLISA showed about 10-fold improved detection sensitivity. With its simple procedure and reliable detection performance in the conventional platform, the proposed immunoassay is expected to have potential applications in clinical diagnostics.