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> Phenomena > Natural Phenomenon or Process > Fluorescence

Fluorescence

Fluorescence is a luminescent phenomenon in which a substance absorbs light or other electromagnetic radiation and then emits light of a different wavelength.
This process is widely utilized in various fields of scientific research, including biology, chemistry, and materials science.
Fluorescence techniques enable the visualization and quantification of a wide range of biological and chemical processes, from cellular dynamics to molecular interactions.
PubCompare.ai's AI-driven platform can help researchers optimize their fluorescence research by easily locating the best protocols from literature, pre-prints, and patents, as well as identifying the top fluorescence techniques and products for their research needs.
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Most cited protocols related to «Fluorescence»

1
Real-time PCR for miRNA Quantification
Real-time PCR was performed using a standard TaqMan® PCR kit protocol on an Applied Biosystems 7900HT Sequence Detection System (P/N: 4329002, Applied Biosystems). The 10 µl PCR included 0.67 µl RT product, 1× TaqMan® Universal PCR Master Mix (P/N: 4324018, Applied Biosystems), 0.2 µM TaqMan® probe, 1.5 µM forward primer and 0.7 µM reverse primer. The reactions were incubated in a 384-well plate at 95°C for 10 min, followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. All reactions were run in triplicate. The threshold cycle (CT) is defined as the fractional cycle number at which the fluorescence passes the fixed threshold. TaqMan® CT values were converted into absolute copy numbers using a standard curve from synthetic lin-4 miRNA.
The method for real-time quantification of pri-miRNA precursors, let-7a-3 and miR-26b, and pre-miRNA precursor miR-30a was described elsewhere (34 (link)).
Chen C., Ridzon D.A., Broomer A.J., Zhou Z., Lee D.H., Nguyen J.T., Barbisin M., Xu N.L., Mahuvakar V.R., Andersen M.R., Lao K.Q., Livak K.J, & Guegler K.J. (2005). Real-time quantification of microRNAs by stem–loop RT–PCR. Nucleic Acids Research, 33(20), e179.
Publication 2005
Fluorescence MicroRNAs Oligonucleotide Primers pre-miRNA Primary MicroRNA Real-Time Polymerase Chain Reaction
2
Systematic Characterization of Mouse Brain
All experimental procedures were approved by the Institutional Animal Care and Use Committee (IACUC) of Allen Institute for Brain Science in accordance with NIH guidelines. All characterization was done using adult mice around ages P56 or older. The mice that were characterized were in a mixed genetic background, containing 50–75% C57BL/6 background and the remainders of 129 or other backgrounds from the various Cre lines. For systematic characterization of fluorescent proteins either by their native fluorescence or IHC, perfused brains were cryosectioned using a tape transfer technique, sections were then DAPI stained directly or following antibody staining, and images were captured using automated fluorescent microscopy. Microtome sections of 100-μm thickness from perfused brains were used for confocal imaging of fluorescently labeled cells. For systematic characterization of gene expression by colorimetric ISH or DFISH, the Allen Institute established pipelines for tissue processing, probe hybridization, image capture and data processing were utilized. Informatics signal identification, mapping, and quantification used the Allen Mouse Brain Atlas spatial mapping platform24 (link), 29 . In this pipeline, image series are preprocessed (white-balanced and cropped), then registered to a three-dimensional informatics reference atlas of the C57BL/6J mouse brain28 . This registration enables data to be displayed in 2D sections or reconstructed 3D volumes.
Madisen L., Zwingman T.A., Sunkin S.M., Oh S.W., Zariwala H.A., Gu H., Ng L.L., Palmiter R.D., Hawrylycz M.J., Jones A.R., Lein E.S, & Zeng H. (2009). A robust and high-throughput Cre reporting and characterization system for the whole mouse brain. Nature neuroscience, 13(1), 133-140.
Publication 2009
Acid Hybridizations, Nucleic Adult Brain Cells Colorimetry DAPI Fluorescence Gene Expression Genetic Background Immunoglobulins Institutional Animal Care and Use Committees Mice, Inbred C57BL Mice, Laboratory Microscopy Microtomy Proteins Tissues
3
Decontamination of Sequencing Data
The contaminant classification methods introduced here are implemented in the open-source decontam R package available from GitHub (https://github.com/benjjneb/decontam) and the Bioconductor repository [35 (link)]. The primary function, isContaminant, implements frequency- and prevalence-based contaminant identification that can be applied to a variety of sequence features including amplicon sequence variants (ASVs), operational taxonomic units (OTUs), taxonomic groups (e.g., genera), orthologous genes, metagenome-assembled-genomes (MAGs), and any other feature with quantitative per-sample relative abundance that is derived from marker-gene or metagenomics sequencing data (see also the “Discussion” section).
The primary input to isContaminant is a feature table of the relative abundances or frequencies of sequence features in each sample (e.g., an OTU table). In addition, isContaminant requires one of two types of auxiliary data for frequency- and prevalence-based contaminant identification, respectively: (1) quantitative DNA concentrations for each sample, often obtained during amplicon or shotgun sequencing library preparation in the form of a standardized fluorescence intensity (e.g., PicoGreen), and/or (2) sequenced negative control samples, preferably DNA extraction controls to which no sample DNA was added. Contaminants identified by decontam can be removed from the feature table with basic R functions described in decontam vignettes.
The isNotContaminant function supports the alternative use case of identifying non-contaminant sequence features in very low-biomass samples (C > S). isNotContaminant implements the prevalence method, but with the standard prevalence score P replaced with 1 − P, so low scores are now those associated with non-contaminants. isNotContaminant does not implement the frequency method for reasons described above and classifies very low prevalence samples conservatively, i.e., as contaminants, as is appropriate for the low-biomass regime.
Davis N.M., Proctor D.M., Holmes S.P., Relman D.A, & Callahan B.J. (2018). Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. Microbiome, 6, 226.
Publication 2018
DNA Library Fluorescence Genes Genetic Diversity Genetic Markers Genome Metagenome PicoGreen
4
Improved qPCR Quantification Method
The expression levels of human family with sequence similarity 73, member B (FAM73B) and GAPDH genes in limited dilution samples (1:10, 1:100, and 1:1000) were analyzed using qPCR. GAPDH was used as an internal control. Referring to the study design in Table 1, FAM73B is the target gene, and GAPDH is the reference gene. The original sample without any dilution is the reference, and a 1:10, 1:100, and 1:1000 dilution of the original sample are the target samples. There are 6 replicates in each combination of gene and dilution. The gene-specific primers were as follows: hgapdh-5′-ATGGAAATCCCATCACCATCTT-3′ and hgapdh-5′-CGCCCCACTTGATTTTGG-3′; hfam73b-5′-CTCCTGCAGGTGGTAGGC-3′ and hfam73b-5′-CAGAGACTGCATCAGAGCCA-3′. mRNA was extracted from human hepatoma (Huh7) cells and used as a template for reverse transcription by superscript III reverse transcriptase purchased from Invitrogen (Carlsbad, CA). All qPCR experiments were performed using the Applied Biosystems Stepone and StepOnePlus Real-Time system (Perkin-Elmer Applied Biosystems). All the amplifications were done using SYBR Green PCR Master Mix (Applied Biosystems). The thermal cycling conditions included an initial denaturation step at 95°C for 10 min, followed by 40 cycles at 95°C for 30s, 60°C for 30s, and 72°C for 30s. Melting curve analysis of every qPCR was conducted after each cycle.
In this study, we try to improve the 2-ΔΔCT method. Our method, called the individual efficiency–corrected calculation method, is shown in Table 2. Unlike the 2-ΔΔCT method, our method accounts for individual efficiencies of samples. We computed the amplification rate E (1 + efficiency) for each sample (Table 2, Eqs. 1-5). Specifically, the method was based on an exponential function, and background fluorescence was included in this function (Eq. 1). Then we took the difference between two consecutive PCR cycles by subtracting the fluorescence of the former cycle from that of the later cycle (Eq. 2). Therefore, the data with n cycles were transformed to data with n−1 cycles. Importantly, background fluorescence was removed. After that, a simple linear regression model (Eq. 4) was applied to the log-transformed equation (Eq. 3). The parameter (β1) estimated using linear regression can be used to calculate E (Eq. 5). To calculate the starting DNA amount (x0), we need to find out the new threshold cycle, CT', and we set the new threshold to T/2 (Eqs. 2 and 6). The fold change of gene expression level was calculated as the relative DNA amount of a target gene in a target sample and a reference sample, normalized to a reference gene (Eq. 7). The DNA amounts of a reference gene in reference and target samples are denoted as x0,A and x0,B, and the amounts of a target gene in the two groups are denoted as x0,C and x0,D, respectively. The derivation of CT' was based on the equal-ratio property of the difference value zk and the cycle m, which is an integer cycle right before CT' (Eqs. 8-9). The fluorescence value zm should be less than the new threshold T/2 because the selected data points had monotone increasing values of zk.
For the 2-ΔΔCT method, we directly used the threshold cycle values automatically generated by the qPCR system. For the individual efficiency corrected calculation method, we selected four successive cycles for every PCR run, the first three of which have the fluorescence values below the threshold and the last of which has a fluorescence value larger than the threshold. Therefore, the target cycles are the rounded threshold cycle and the former three cycles, or the rounded threshold cycle and the former two cycles plus the latter one.
In the individual efficiency corrected calculation method, we calculated PCR amplification efficiency for every sample. To reduce potential variation, we then took the mean of the efficiencies for the 6 replicates under each condition, which is a combination of gene and dilution. Hence, the 6 replicates had the same efficiency for further calculation, but each combination (for example, the combination of FAM73B and a 1:10 dilution) had a different efficiency.
Because the 2-ΔΔCT method and our method are relative quantification strategies, it is difficult to assess their accuracy. This is why we planned to use a series of dilutions of the original sample to evaluate the accuracy of these two methods based on the pattern of the estimates. According to the experimental design, there were two trends in the estimates. First, for each gene, the ratios of the initial DNA amount were 1, 1:10 (0.1), 1:100 (0.01), and 1:1000 (0.001), corresponding to the four dilution conditions. The second trend was that the relative gene amounts (FAM73B/GAPDH) with respect to the four dilution conditions were the same, with a ratio of 1: 1: 1: 1 if the original sample without dilution was set to 1. The precision of the methods was then analyzed by computing coefficients of variation (CVs). The equation is:
where s and x̄ are the standard deviation and the mean of the 6 replicates in each combination of gene and dilution.
Rao X., Huang X., Zhou Z, & Lin X. (2013). An improvement of the 2ˆ(–delta delta CT) method for quantitative real-time polymerase chain reaction data analysis. Biostatistics, bioinformatics and biomathematics, 3(3), 71-85.
Publication 2013
Fluorescence GAPDH protein, human Gene Expression Genes Genes, vif Hepatocellular Carcinomas Homo sapiens Oligonucleotide Primers Reverse Transcription RNA, Messenger RNA-Directed DNA Polymerase SYBR Green I Technique, Dilution Transcriptase Transcription, Genetic
5
Multispecies Live-Cell Imaging and Analysis
C. crescentus, B. subtilis, A. biprosthecum, Rhodomicrobium sp, and P. hirshii were grown in PYE14 (link) at 30°C. A. tumefaciens, S. venezuelae, L. lactis, were grown in LB15 (link) at 30°C and E. coli was grown in LB15 (link) at 37°C. M. xanthus were grown at 32°C in CYE16 (link). S. pneumonia were grown at 37°C in THY17 . Rhodopseudomonas palustris CGA009 was grown anaerobically in defined mineral medium (PM)18 supplemented with 10 mM succinate and incubated at 30°C with constant illumination from a 60 W incandescent light bulb.
Phase and fluorescence time-lapse imaging was performed on a Nikon Ti-E inverted microscope, equipped with a Plan Apo 60×, 1.40 NA, Oil, Ph3 DM objective and 1.5× magnifier. Images were acquired every 5 min, and fluorescent proteins were illuminated with a Lumencor Spectra × light engine equipped with excitation filters 470/24 (GFP), 510/25 (YFP) or 575/25 (mCherry), Chroma emission filters 510/40 (GFP), 545/30 (YFP), 530/60 (mCherry) and either a quad polychroic DAPI/FITC/Cy3/Cy5 or triple polychroic CFP/YFP/mCherry cube for Lumencor SpectraX. Images were acquired using an Andor iXon3 DU885 EM CCD camera driven by NIS Elements Advanced Research software (Nikon, Melville, NY)
Cultures from strain YB4667 CB15::pvan-ftsZ-yfp were grown in PYE medium at 30°C and induced for 2 hours with 0.5 mM vanillic acid to express FtsZ-YFP. Exponentially growing cells from this culture were spotted onto a 0.8 mm thick 1% agarose pad made with PYE medium containing 0.5 mM vanillic acid and timelapse images were acquired every 5 minutes from 16 different slide positions for 54 time points. For cell division inhibition, 30 µg/ml of cephalexin was added to the agarose pad during the imaging period.
For precision assessment of MicrobeJ, Molecular Probes FluoSpheres carboxylate-modified microspheres (F8823), 1± 0.0480 µm lot #1761288 were spotted onto a 1% agarose pad made with deionized water and images were acquired for 30 ms using the same microscope, camera and objective as cells.
Ducret A., Quardokus E.M, & Brun Y.V. (2016). MicrobeJ, a tool for high throughput bacterial cell detection and quantitative analysis. Nature microbiology, 1(7), 16077.
Publication 2016
Apolipoproteins A Cell Culture Techniques Cells Cephalexin DAPI Division, Cell Escherichia coli Fluorescein-5-isothiocyanate Fluorescence Incandescence Light Medulla Oblongata Microscopy Microspheres Minerals Molecular Probes Pneumonia Proteins Psychological Inhibition Rhodomicrobium Rhodopseudomonas palustris Sepharose Strains Succinate Vanillic Acid

Most recents protocols related to «Fluorescence»

1
PD-1/PD-L1 Blocking Antibody Assay
Not available on PMC !

Example 10

This example provides in vitro IC50 data for the blocking of the interaction between recombinant human PD-1 (PD-1-Fc Chimera; Sino Biologics) and human PD-L1 expressed CHO cells by anti-PD-L1 antibody G12. Here, CHO cells expressing PD-L1 were pre-incubated with G12 prior to the addition of rhPD-1-Fc chimeric protein. After incubation and washing, PD-1 binding to cell surface expressed PD-L1 was detected using an Alexa-Fluor 647 tagged anti-PD-1 antibody by flow cytometry (Intellicyt HTFC; FL-4H). This example shows that anti-PD-L1 monoclonal antibody G12 was able to inhibit efficiently the binding of PD-1 to PD-L1 expressed on the surface of CHO cells.

Results: As shown in FIG. 8 and Table 4, the IC50 for blocking of the PD-1/PD-L1 cellular interaction by G12 is 1.76E-09 M. Data was collected on the Intellicyt HTFC flow cytometer, processed using FlowJo software, and analyzed and plotted in Graph Pad Prizm using non-linear regression fit. Data points are shown as the median fluorescence detected in the FL-4H channel+/−Std Error.

TABLE 4
G12
Inhibition of PD-1/PD-L1CHO-PD-L1/1.76E−09
Interaction IC50 (M)rhPD-1-Fc

US11878058B2. Antigen binding proteins that bind PD-L1 (2024-01-23). Sorrento Therapeutics, Inc. [US]. Inventors: Heyue Zhou [US], Randy Gastwirt [US], Barbara A. Swanson [US], John Dixon Gray [US], Gunnar F. Kaufmann [US].
Patent 2024
Alexa Fluor 647 Antibodies, Anti-Idiotypic Antigens Binding Proteins Biological Factors CD274 protein, human Cell Communication Cells Chimera CHO Cells Flow Cytometry Fluorescence Homo sapiens Immunoglobulins isononanoyl oxybenzene sulfonate Monoclonal Antibodies Proteins Psychological Inhibition
2
Translocation of Surface Lipoproteins in E. coli
Not available on PMC !

Example 6

TbpB and NMB0313 genes were amplified from the genome of Neisseria meningitidis serotype B strain B16B6. The LbpB gene was amplified from Neisseria meningitidis serotype B strain MC58. Full length TbpB was inserted into Multiple Cloning Site 2 of pETDuet using restriction free cloning ((F van den Ent, J. Löwe, Journal of Biochemical and Biophysical Methods (Jan. 1, 2006)).). NMB0313 was inserted into pET26, where the native signal peptide was replaced by that of pelB. Mutations and truncations were performed on these vectors using site directed mutagenesis and restriction free cloning, respectively. Pairs of vectors were transformed into E. coli C43 and were grown overnight in LB agar plates supplemented with kanamycin (50 μg/mL) and ampicillin (100 μg/mL).

tbpB genes were amplified from the genomes of M. catarrhalis strain 035E and H. influenzae strain 86-028NP and cloned into the pET52b plasmid by restriction free cloning as above. The corresponding SLAMs (M. catarrhalis SLAM 1, H. influenzae SLAM1) were inserted into pET26b also using restriction free cloning. A 6His-tag was inserted between the pelB and the mature SLAM sequences as above. Vectors were transformed into E. coli C43 as above.

Cells were harvested by centrifugation at 4000 g and were twice washed with 1 mL PBS to remove any remaining growth media. Cells were then incubated with either 0.05-0.1 mg/mL biotinylated human transferrin (Sigma-aldrich T3915-5 MG), α-TbpB (1:200 dilution from rabbit serum for M. catarrhalis and H. influenzae; 1:10000 dilution from rabbit serum for N. meningitidis), or α-LbpB (1:10000 dilution from rabbit serum-obtained a gift from J. Lemieux) or α-fHbp (1:5000 dilution from mouse, a gift from D. Granoff) for 1.5 hours at 4° C., followed by two washes with 1 mL of PBS. The cells were then incubated with R-Phycoerythrin-conjugated Streptavidin (0.5 mg/ml Cedarlane) or R-phycoerythrin conjugated Anti-rabbit IgG (Stock 0.5 mg/ml Rockland) at 25 ug/mL for 1.5 hours at 4° C. The cells were then washed with 1 mL PBS and resuspended in 200 uL fixing solution (PBS+2% formaldehyde) and left for 20 minutes. Finally, cells were washed with 2×1 mL PBS and transferred to 5 mL polystyrene FACS tubes. The PE fluorescence of each sample was measured for PE fluorescence using a Becton Dickinson FACSCalibur. The results were analyzed using FLOWJO software and were presented as mean fluorescence intensity (MFI) for each sample. For N. meningtidis experiments, all samples were compared to wildtype strains by normalizing wildtype fluorescent signals to 100%. Errors bars represent the standard error of the mean (SEM) across three experiments. Results were plotted statistically analysed using GraphPad Prism 5 software. The results shown in FIG. 6 for the SLPs, TbpB (FIG. 6A), LbpB. (FIG. 6B) and fHbp (FIG. 6C) demonstrate that SLAM effects translocation of all three SLP polypeptides in E. coli. The results shown in FIG. 10 demonstrate that translocation of TbpB from M. catarrhalis (FIG. 10C) and in H. influenzae (FIG. 10D) in E. coli require the co-expression of the required SLAM protein (Slam is an outer membrane protein that is required for the surface display of lipidated virulence factors in Neisseria. Hooda Y, Lai C C, Judd A, Buckwalter C M, Shin H E, Gray-Owen S D, Moraes T F. Nat Microbiol. 2016 Feb. 29; 1:16009).

US11872275B2. SLAM polynucleotides and polypeptides and uses thereof (2024-01-16). ENGINEERED ANTIGENS INC. [CA]. Inventors: Trevor F. Moraes [CA], Christine Chieh-Lin Lai [CA], Yogesh Hooda [CA], Andrew Judd [CA], Anthony B. Schryvers [CA], Scott D. Gray-Owen [CA].
Patent 2024
ADRB2 protein, human Agar Ampicillin anti-IgG Cells Centrifugation Cloning Vectors Culture Media Escherichia coli Fluorescence Formaldehyde Genes Genome Haemophilus influenzae Homo sapiens Kanamycin Lipoproteins Membrane Proteins Moraxella catarrhalis Mus Mutagenesis, Site-Directed Mutation Neisseria Neisseria meningitidis Phycoerythrin Plasmids Polypeptides Polystyrenes prisma Rabbits Serum Signaling Lymphocytic Activation Molecule Family Member 1 Signal Peptides Strains Streptavidin Technique, Dilution Transferrin Translocation, Chromosomal Virulence Factors
3
Multicolor Imaging of Zebrafish Embryos
Not available on PMC !

Example 2

About 5 μM fluorescein (F1300, Invitrogen, Carlsbad, CA) solution in ethanol was prepared. For imaging, the solution was transferred into a sealed 10 mm glass bottom dish (P35G-1.5-10-c, MatTek Corporation, Ashland, MA, USA) and mounted in an inverted confocal microscope. Imaging was performed on a Zeiss LSM780 inverted confocal microscope with QUASAR detector (Carl Zeiss, Jena, Germany). A typical dataset consists of 32 images, each of dimensions 512×512 pixels, corresponding to different wavelengths from about 410.5 nm to about 694.9 nm with about 8.9 nm bandwidth. The measurement is repeated 10 times using C-Apochromat 40×/1.20 W Korr Zeiss objective at any given imaging parameter. Fluorescein was imaged with about 488 nm laser at different acquisition parameters (Table 1).

For in vivo imaging 5-6 zebrafish embryos at appropriate stage were placed into about 1% agarose (Catalog No. 16500-100, Invitrogen™) moulds created in an imaging dish with #1.5 coverglass bottom, (Catalog No. D5040P, WillCo Wells) using a custom designed negative plastic mould [29]. Embryos were immobilized by adding about 2 ml of about 1% UltraPure™ Low Melting Point Agarose (Catalog No. 16520-050, Invitrogen™) solution prepared in about 30% Danieau (about 17.4 mM NaCl, about 210 μM KCl, about 120 μM MgSO4.7H2O, about 180 μM Ca(NO3)2, about 1.5 mM HEPES buffer in water, pH about 7.6) with about 0.003% PTU and about 0.01% tricaine. This solution was then added on top of the embryos already placed in the mold. Following solidification of agarose at room temperature (1-2 minutes), the imaging dish was filled with about 30% Danieau solution and about 0.01% Tricaine, at about 28.5° C. Subsequent imaging was performed on an inverted confocal microscope by positioning the petridish appropriately on the microscope stage. Samples were obtained by crossing Gt(desm-citrine)ct122a/+ with Tg(kdrl:eGFP) fish for two color imaging. Samples with four fluorescent proteins result from same crossing followed by injection of about 100 pg per embryo of mRNA encoding H2B-cerulean and membrane-mCherry. Samples of Gt(desm-citrine)ct122a/+;Tg(kdrl:eGFP) were imaged with about 488 nm laser to excite both Citrine and eGFP and a narrow about 488 nm dichroic to separate excitation and fluorescence emission. Samples of Gt(desm-citrine)ct122a/+;Tg(kdrl:eGFP) with H2B-cerulean and membrane-mCherry labels were imaged with about 458 nm laser to excite Cerulean, eGFP and Citrine with a narrow about 488 nm dichroic, following an about 561 nm laser to excite mCherry with an about 458-561 nm dichroic.

For in vivo time-lapse imaging 5-6 zebrafish at appropriate stage were immobilized in an imaging dish with #1.5 coverglass bottom using about 0.5% Low Melting Point Agarose agarose (same as above) to allow for development and with about 0.003% PTU and about 0.01% tricaine. Subsequent imaging was performed on the same confocal-two photon inverted microscope at about 28.5° C. A solution of Egg Water was added every hour to the imaging dish to ensure proper hydration of the sample. Samples with five fluorescent proteins were obtained by crossing Tg(kdrl: eGFP) with Tg(ubiq:membrane-Cerulean-2a-H2B-tdTomato) zebrafish followed by injection of about 120 pg and about 30 pg per embryo of mRNA encoding Rab9-YFP and Rab11-mCherry, respectively. Volumetric data was acquired using about 950 nm to excite Cerulean, eGFP, YFP and (weakly) tdTomato with a 760+ bandpass filter, following an about 561 nm laser to excite mCherry and tdTomato with an about 458-561 nm dichroic.

Table 3 provides the detailed description of the imaging parameters used for all images presented in this work.

US11869176B2. Hyperspectral imaging system (2024-01-09). UNIVERSITY OF SOUTHERN CALIFORNIA [US]. Inventors: Wen Shi [US], Eun Sang Koo [US], Scott E. Fraser [US], Francesco Cutrale [US].
Patent 2024
Buffers Embryo Ethanol Fishes Fluorescein Fluorescence Fungus, Filamentous HEPES Hyperostosis, Diffuse Idiopathic Skeletal Microscopy Microscopy, Confocal Proteins RNA, Messenger Sepharose Sodium Chloride Sulfate, Magnesium tdTomato Tissue, Membrane tricaine Zebrafish
4
Identifying SLAM-Dependent Surface Lipoproteins
Not available on PMC !

Example 8

In selecting genomes for a given bacterial species where a SLAM homolog was identified, preference was given to reference genomes that contained fully sequenced genomes. SLAM homologs were identified using iterative Blast searches into closely related species to Neisseria to more distantly related species. For each of the SLAM homologs identified in these species, the corresponding genomic record (NCBI genome) was used to identify genes upstream and downstream along with their corresponding functional annotations (NCBI protein database, Ensembl bacteria). In a few cases, no genes were predicted upstream or downstream of the SLAM gene as they were too close to the beginning or end of the contig, respectively, and thus these sequences were ignored.

Neighbouring genes were analyzed for 1) an N-terminal lipobox motif (predicted using LipoP, SignalP), and 2) a solute binding protein, Tbp-like (InterPro signature: IPR or IPR011250), or pagP-beta barrel (InterPro signature: IPR011250) fold. If they contained these elements, we identified the adjacent genes as potential SLAM-dependent surface lipoproteins.

A putative SLAM (PM1515, SEQ ID NO: 1087) was identified in Pasteurella multocida using the Neisseria SLAM as a search. The putative SLAM (PM1515, SEQ ID NO: 1087) was adjacent to a newly predicted lipoprotein gene with unknown function (PM1514, SEQ ID NO: 1083) (FIG. 11A). The putative SLAM displayed 32% identity to N. meningitidis SLAM1 while the SLP showed no sequence similarity to known SLAM-dependent neisserial SLPs.

The putative SLAM (PM1515, SEQ ID NO: 1087) and its adjacent lipoprotein (PM1514, SEQ ID NO: 1083) were cloned into pET26b and pET52b, respectively, as previously described and transformed into E. coli C43 and grown overnight on LB agar supplemented with kanamycin (50 ug/ml) and ampicillin (100 ug/ml).

Cells were grown in auto-induction media for 18 hours at 37 C and then harvested, washed twice in PBS containing 1 mM MgCl2, and labeled with α-Flag (1:200, Sigma) for 1 hr at 4 C. The cells were then washed twice with PBS containing 1 mM MgCl2 and then labeled with R-PE conjugated α-mouse IgG (25 ug/mL, Thermo Fisher Scientific) for 1 hr at 4 C. following straining, cells were fixed in 2% formaldehyde for 20 minutes and further washed with PBS containing 1 mM MgCl2. Flow Cytometry was performed with a Becton Dickinson FACSCalibur and the results were analyzed using FLOWJO software. Mean fluorescence intensity (MFI) was calculated using at least three replicates was used to compare surface exposure the lipoprotein in strains either containing or lacking the putative SLAM (PM1515) and are shown in FIG. 11C and FIG. 11D. PM1514 could be detected on the surface of E. coli illustrating i) that SLAM can be used to identify SLPs and ii) that SLAM is required to translocate these SLPs to the surface of the cell—thus identifying a class of proteins call “SLAM-dependent surface lipoproteins”. Antibodies were raised against purified PmSLP (PM1514) and the protein was shown to be on the surface of Pasteurella multocida via PK shaving assays.

US11872275B2. SLAM polynucleotides and polypeptides and uses thereof (2024-01-16). ENGINEERED ANTIGENS INC. [CA]. Inventors: Trevor F. Moraes [CA], Christine Chieh-Lin Lai [CA], Yogesh Hooda [CA], Andrew Judd [CA], Anthony B. Schryvers [CA], Scott D. Gray-Owen [CA].
Patent 2024
Agar Ampicillin Antibodies Bacteria Binding Proteins Biological Assay Cells Escherichia coli Flow Cytometry Fluorescence Formaldehyde Genes Genome Kanamycin Lipoprotein (a-) Lipoproteins Magnesium Chloride Mus Neisseria Neisseria meningitidis Pasteurella multocida Proteins Staphylococcal Protein A Strains
5
Fluorescence-based Dichloromethane Detection
Not available on PMC !

Example 5

To test the cycle performance of the compound in the fluorescence detection of dichloromethane vapor, the related investigations were performed. The air and air with dichloromethane vapor were manually controlled to enter the cuvette by using the instrument shown in FIG. 6 to test the cycle performance, and the time interval between the two gases was 50 seconds. The test results are shown in FIG. 8. The compound shows an excellent cycle performance in response to dichloromethane vapor. After 20 rounds of cycle test, it still retains a high sensitivity, and the fluorescence intensity has no significant change before and after the response to dichloromethane vapor.

US11873449B2. Fluorescent chromic material, preparation method and use thereof (2024-01-16). SOOCHOW UNIVERSITY [CN]. Inventors: Jianping Lang [CN], Chunyu Liu [CN], Liang Chen [CN], Chunyan Ni [CN].
Patent 2024
Fluorescence Gases Hypersensitivity Methylene Chloride Neoplasm Metastasis

Top products related to «Fluorescence»

1
Facscalibur by BD
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The FACSCalibur is a flow cytometry system designed for multi-parameter analysis of cells and other particles. It features a blue (488 nm) and a red (635 nm) laser for excitation of fluorescent dyes. The instrument is capable of detecting forward scatter, side scatter, and up to four fluorescent parameters simultaneously.
2
Facscalibur flow cytometer by BD
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The FACSCalibur flow cytometer is a compact and versatile instrument designed for multiparameter analysis of cells and particles. It employs laser-based technology to rapidly measure and analyze the physical and fluorescent characteristics of cells or other particles as they flow in a fluid stream. The FACSCalibur can detect and quantify a wide range of cellular properties, making it a valuable tool for various applications in biology, immunology, and clinical research.
3
Facscanto 2 by BD
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The FACSCanto II is a flow cytometer instrument designed for multi-parameter analysis of single cells. It features a solid-state diode laser and up to four fluorescence detectors for simultaneous measurement of multiple cellular parameters.
4
4 6 diamidino 2 phenylindole (dapi) by Merck Group
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DAPI is a fluorescent dye that binds strongly to adenine-thymine (A-T) rich regions in DNA. It is commonly used as a nuclear counterstain in fluorescence microscopy to visualize and locate cell nuclei.
5
Trizol reagent by Thermo Fisher Scientific
Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand
TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
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4 6 diamidino 2 phenylindole (dapi) by Thermo Fisher Scientific
Sourced in United States, Germany, United Kingdom, Japan, China, Canada, Italy, Australia, France, Switzerland, Spain, Belgium, Denmark, Panama, Poland, Singapore, Austria, Morocco, Netherlands, Sweden, Argentina, India, Finland, Pakistan, Cameroon, New Zealand
DAPI is a fluorescent dye used in microscopy and flow cytometry to stain cell nuclei. It binds strongly to the minor groove of double-stranded DNA, emitting blue fluorescence when excited by ultraviolet light.
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Lsm 710 by Zeiss
Sourced in Germany, United States, United Kingdom, Japan, Switzerland, France, China, Canada, Italy, Spain, Singapore, Austria, Hungary, Australia
The LSM 710 is a laser scanning microscope developed by Zeiss. It is designed for high-resolution imaging and analysis of biological and materials samples. The LSM 710 utilizes a laser excitation source and a scanning system to capture detailed images of specimens at the microscopic level. The specific capabilities and technical details of the LSM 710 are not provided in this response to maintain an unbiased and factual approach.
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Fluorescence microscope by Olympus
Sourced in Japan, United States, Germany, China, Italy, United Kingdom, Denmark, Switzerland, France
The Olympus Fluorescence Microscope is an optical microscope that uses fluorescence to visualize and analyze samples. It illuminates the specimen with light of a specific wavelength, causing fluorescent molecules within the sample to emit light at a different wavelength, which is then detected and displayed.
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Triton x 100 by Merck Group
Sourced in United States, Germany, United Kingdom, Italy, China, Japan, France, Canada, Sao Tome and Principe, Switzerland, Macao, Poland, Spain, Australia, India, Belgium, Israel, Sweden, Ireland, Denmark, Brazil, Portugal, Panama, Netherlands, Hungary, Czechia, Austria, Norway, Slovakia, Singapore, Argentina, Mexico, Senegal
Triton X-100 is a non-ionic surfactant commonly used in various laboratory applications. It functions as a detergent and solubilizing agent, facilitating the solubilization and extraction of proteins and other biomolecules from biological samples.
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Cellquest software by BD
Sourced in United States, Germany, United Kingdom, Italy, Canada, China, Japan, Belgium, France, Spain, Switzerland, Poland, Uruguay, Denmark, Singapore
CellQuest software is a data acquisition and analysis software designed for flow cytometry applications. It provides tools for acquiring, processing, and analyzing flow cytometry data.

More about "Fluorescence"

Fluorescence is a luminescent phenomenon where a substance absorbs light or electromagnetic radiation and then emits light at a different wavelength.
This process is widely utilized in various scientific fields, such as biology, chemistry, and materials science.
Fluorescence techniques enable the visualization and quantification of a diverse range of biological and chemical processes, from cellular dynamics to molecular interactions.
The FACSCalibur flow cytometer and FACSCanto II are popular instruments used in fluorescence-based research, allowing for the analysis and sorting of cells based on their fluorescent properties.
DAPI, a fluorescent dye, is commonly used to stain and visualize DNA, while the TRIzol reagent is often employed for the extraction and purification of RNA.
The LSM 710 is a powerful fluorescence microscope that enables high-resolution imaging of fluorescently labeled samples.
Triton X-100, a non-ionic detergent, is frequently used in fluorescence-based assays to permeabilize cell membranes and facilitate the introduction of fluorescent probes.
CellQuest software is a widely used tool for the analysis and interpretation of data generated from flow cytometry experiments.
PubCompare.ai's AI-driven platform can help researchers optimize their fluorescence research by easily locating the best protocols from literature, preprints, and patents, as well as identifying the top fluorescence techniques and products for their research needs.
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