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59 results for “Fluorescent protein”
Dataset for "Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms"
<p>Dataset that supports the observation, characterization and application of the blue-shift photoconversion of the near infrared proteins, miRFPs, reported in the manuscript: "Blue-shift photoconversion of near-infrared fluorescent proteins for labeling and tracking in living cells and organisms". The data references to the specific figures and graphs in the manuscript.</p>
Supplementary Material: Fluorescent Protein‐Tagged Sindbis Virus E2 Glycoprotein Allows Single Particle Analysis of Virus Budding from Live Cells
<p>Supplementary Videos for <em>Viruses</em> <strong>2015</strong>, <em>7</em>(12), 6182-6199; doi:10.3390/v7122926, http://www.mdpi.com/1999-4915/7/12/2926:</p> <p><strong>Video S1A</strong> BHK cells infected with mCherry-E2 virus at 3 h p.i. Glycoprotein containing vesicles are transported to the PM from where individual virions bud out. White arrow point to budding virions. Overall amount of glycoproteins present on the PM and the number of virus particles budding out are relatively reduced compared to the late stage of infection. Images were acquired at a rate of 0.99 fps and 75 frames were acquired. Video was generated using these images and played at a rate of 5 fps. Image acquisition time is shown as Time: hour: minute: second: millisecond (h:min:sec:msec ) and the scale bar represents 10 μm.</p> <p><strong>Video S1B </strong>Enlarged area of video S1A showing budding virus particles from PM. White arrow indicates single particle post-budding moving away from the cell. Images were acquired at a rate of 0.99 fps and 75 frames were acquired. Video was generated using these images and played at a rate of 5 fps. Image acquisition time is shown as Time: hour: minute: second: millisecond (h:min:sec:msec ) and the scale bar represents 10 μm.</p> <p><strong>Video S2A</strong> Virus budding and single particle movement associated with filopodial extensions observed from mCherry-E2 virus-infected BHK cells at 6 h p.i. Glycoprotein containing vesicle transport to the PM is also observed. Budded virions travel along the periphery of filopodia and are released from filopodial extensions to the surrounding media. Image acquisition was at a rate of 1 fps and 285 frames were acquired. Movie was generated using these images and played at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S2B</strong> Enlarged area of video S2A showing budding virus particles from filopodia. White arrow indicates virus budding from filopodial extensions. Images were acquired at a rate of 1 fps and the acquired 285 frames were used to generate the video at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S3</strong> BHK cells transfected with RNA from a non-budding cdE2 mutant <sub>416</sub>CC<sub>417</sub>/A2 mCherry-E2 virus. This non-budding mutant is unable to release fluorescent virus particles from the infected cells. The video shows the absence of fluorescent virus particle budding from the PM at 6 h post transfection even though the PM and filopodial extensions contain mCherry-E2. Despite the transport of glycoproteins to the PM, no fluorescent particles were released into the media. Yellow arrows point toward filopodial extensions. For the video, 304 images were acquired at a rate of 0.98 fps and the video was generated using the acquired images at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S4</strong> BHK cells transfected with RNA from an E1 Fusion loop (G91D) mutant of mCherry-E2 virus at 6 h post transfection. This non-fusing mutant produces fluorescent virus particles at a slower rate compared to WT that are unable to fuse after entering a new cell. White arrow points to fluorescent particles that are releasing into the media from filopodial extensions. Yellow arrow represents a fluorescent particle that had entered an adjacent un-transfected cell. A total of 149 images were acquired at a rate of 0.98 fps. Video was generated using these images at a rate of 7 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p> </p> <p><strong>Video S5A</strong> Glycoprotein E2 (mCherry-E2; red) colocalizing with Golgi stain (green) in BHK cells infected with mCherry-E2 virus and stained with BODIPY FL C5 ceramide at 5 h p.i. and imaged at 6 h p.i. Glycoprotein-containing red vesicles originate from Golgi as evidenced from the colocalization of red and green and these vesicles display anterograde transport to the PM and the virus particles are released by budding from the PM. Fluorescent particles are also seen budding from filopodial extensions (white arrows). Images were acquired at a rate of 0.13 fps for 295 seconds. Video was generated using these acquired images at a rate of 5 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p><strong>Video S5B</strong> An enlarged area of the video S5A near the white arrow showing movement of particles on filopodial extensions between two cells. Movie was played at a rate of 5 fps. Image acquisition time is shown as Time: h:min:sec:msec and the scale bar represents 10 μm.</p> <p> </p> <p> </p>
Dataset to manuscript entitled "Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies" submitted to Scientifc Reports
<p><strong>This folder contains all raw data underlying the results presented in a manuscript, submitted to</strong><strong> </strong><strong><em>Scientifc Reports, </em>and entitled</strong><strong>:</strong></p> <p><strong><em>Non-fluorescent transient states of tyrosine - a basis for label-free protein conformation and interaction studies</em></strong></p> <p> </p> <p><strong>Authored by:</strong></p> <p><strong>Niusha Bagheri <sup>1</sup>, Hongjian Chen <sup>1</sup>, Mihailo Rabasovic <sup>2</sup>, Jerker Widengren <sup>1,*</sup></strong></p> <p><sup>1 </sup>Royal Institute of Technology (KTH), Experimental Biomolecular Physics, Dept. Applied Physics, Albanova University Center 106 91 Stockholm, Sweden</p> <p><sup>2 </sup>Laboratory for Biophysics, Institute of Physics Belgrade, Pregrevica 118<br>11080 Zemun-Belgrade, Serbia</p> <p>* Corresponding author (jwideng@kth.se)</p> <p><strong> </strong></p> <p><strong>The data files are grouped into the different techniques used to generate them, and refer to the figures/tables in the manuscript where the extracted results are presented. </strong></p> <p> </p> <p><strong>ABSTRACT</strong></p> <p>The amino acids tryptophan, tyrosine, and phenylalanine have been extensively used for different label-free protein studies, based on the intensity, lifetime, wavelength and/or polarization of their emitted fluorescence. Like most fluorescent organic molecules, these amino acids also tend to undergo transitions into dark meta-stable states, such as triplet and photo-radical states. While this may be perceived as a problem, these transitions are also highly environment-sensitive and can be used as an additional set of parameters, reflecting interactions, folding states, and immediate environments around the proteins. In this work, we applied the transient state monitoring (TRAST) technique, analyzing the average intensity of tyrosine emission under different excitation modulations, to characterize the photo physics of tyrosine for such readout purposes. By investigating how the dark state transitions of tyrosine varied with excitation intensity and solvent conditions we established a photophysical model for tyrosine. Next, we studied Calmodulin (containing two tyrosines), which upon calcium binding takes a more folded conformation. From these TRAST experiments, performed with 280nm time-modulated excitation, we show that tyrosine dark state transitions clearly change with the calmodulin conformation, and may thus represent a useful source of information for (label-free) analyses of protein conformations and interactions.</p>
Fig. 15 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 15. Trychosis breviterebratus sp. nov. (A-F, KPM-NK 75758) ― A, lateral habitus; B, dorsal habitus; C, frons, frontal view; D, head and mesosoma, lateral view; E, propodeum, dorsal view; F, right wings.
Fig. 14. Hylophasma luica Sheng, Li in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 14. Hylophasma luica Sheng, Li & Wang, 2019 (A-D, KPM-NK 75813; E, KPM-NK 75821) and Picardiella melanoleuca (Gravenhorst, 1829)(F-J, KPM-NK 75744) ― A, E, F, lateral habitus; B, G, dorsal habitus; C, H, head, frontal view; D, J, right fore wing; I, propodeum, dorsal view.
Fig. 13. Hoplocryptus sumiyona Uchida, 1956 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 13. Hoplocryptus sumiyona Uchida, 1956 (A-C, KPM-NK 76581) and H. toshimensis sp. nov. (E-I, KPM-NK 75797) ― A, E, dorsal habitus; B, F, head, frontal view; C, head and mesosoma, dorso-lateral view; D, lateral habitus; G, propodeum, dorsal view; H, right fore wing; I. metasoma, dorsal view.
Fig. 12 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 12. Hoplocryptus pini (Momoi, 1973) (A, D, F, KPM-NK 76578; B, E, KPM-NK 75780; C, G, KPM-NK 75774; H-J, 76580) ― A-C, H, lateral habitus; D, E, I, head, mesosoma and metasoma, dorsal view; F, J, head, frontal view; G, propodeum, dorsso-lateral view.
Fig. 10 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 10. Hoplocryptus ezoensis sp. nov. (A, C-F, KPM-NK 75799; B, KPM-NK 75802) and Ho. intermedius sp. nov. (G-K, KPM-NK 75806; L, M, KPM-NK 76582) ― A, G, L, lateral habitus; B, C, dorsal habitus; D, H, M, head, frontal view; E, J, propodeum, dorsal (E) and dorso-lateral (J) view; I, head and mesoscutum, dorso-lateral view; K, right fore wing.
Fig. 6. Caenocryptoides convergens Momoi, 1966 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 6. Caenocryptoides convergens Momoi, 1966 (A-C, TMNH) and Cryptus daidaigaster sp. nov. (D-J, NIAES) ― A, D, I, lateral habitus; B, E, head, mesosoma and metasoma, dorso-lateral view; C, F, J, head, frontal view; G, propodeum, dorsal view; H, right wings.
Fig. 2 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 2. Aritranis kuro sp. nov. (A, B, KPM-NK 75832); Buathra nipponica sp. nov. (C, D, KPM-NK 75746), Glabridorsum japonicum sp. nov. (E, KPM-NK 75742), Hoplocryptus ezoensis sp. nov. (F, KPM-NK 75799), Ho. intermedius sp. nov. (G, KPM-NK 75804), Ho. japonicus sp. nov. (H, KPM-NK 75771), Ho. maculatus sp. nov. (I, KPM-NK 75790, J, KPM-NK 75781, K, KPM-NK 75783), Hylophasma luica Sheng, Li & Wang, 2019 (L, M, KPM-NK 75813) and Trychosis breviterebratus sp. nov. (N, KPM-NK 75748), females ― A, F, G, H, M, propodeum and T I, dorsal (A, H, M) and lateral (F, G) view; B, E, L, T I, lateral view; C, I, propodeum, lateral (C) and dorsal (I) view; D, T I, lateral view; J, K, area basalis and part of anterior transverse carina of propodeum; N, metasoma, lateral view. Surface sculpture of right half of Fig. 2A omitted.
Fig. 1 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 1. Aritranis kuro sp. nov. (A, KPM-NK 75838); Buathra nipponica sp. nov. (B, C, KPM-NK 75746), Hoplocryptus ezoensis sp. nov. (D, KPM-NK 75799), Ho. ashoroensis sp. nov. (E, NIAES), Ho. intermedius sp. nov. (F, KPM-NK 75804), Ho. japonicus sp. nov. (G, KPM-NK 75771), Ho. maculatus sp. nov. (H, KPM-NK 75781), Ho. toshimensis sp. nov. (I, KPM-NK 75797), Hylophasma luica Sheng, Li & Wang, 2019 (J, K, KPM-NK 75813) and Trychosis breviterebratus sp. nov. (L-P, KPM-NK 75748), females ― A-D, J-M, head, frontal (A, B, D, J, L), lateral (C) and dorsal (K, M) view; E-I, apical margin of clypeus, frontal view; K, left mandible; O, left fore femur, anterior view; lower part of epicnemial carina, lateral view.
Fig. 5 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 5. Buathra nipponica sp. nov. (A-G, KPM-NK 75746; H, I, KPM-NK 75747) ― A, lateral habitus; B, mesosoma, lateral view; C, head, mesosoma and metasoma, dorsal view; D, frons, frontal view; E, propodeum, dorsal view; F, right fore wing; G, apex of metasoma, dorso-lateral view.
Fig. 9 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 9. Gotra elegans sp. nov. (A, C, D, KPM-NK 75822; B, E, KPM-NK 75823) and Hoplocryptus ashoroensis sp. nov. (F-J, NIAES) ― A, C, lateral habitus; B, dorsal habitus; C, H, head, frontal view; D, head, mesoscutum and scutellum, dorsal view; E, I, propodeum, dorsal view; J, right fore wing.
Fig. 4. Agrothereutes minousubae Nakanishi, 1965 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 4. Agrothereutes minousubae Nakanishi, 1965 (A, B, KPM-NK 76585; C, D, KPM-NK 76590) and Aritranis kuro sp. nov. (E, G, I, KPM-NK 75824; F, H, KPM-NK 75825; J, K, KPM-NK 76577) ― A, C, E, J, lateral habitus; B, tegula and humeral plate (red arrow), dorso-lateral view; D, G, K, head, frontal view; F, dorsal habitus; H, propodeum, dorsal view; I, right wings.
Fig. 7. Gambrus homonae Sonan, 1930 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 7. Gambrus homonae Sonan, 1930 (A, KPM-NK 76572; B-D, 76568; E, KPM-NK 76573) ― A, E, lateral habitus; B, head, frontal view; C, propodeum, dorsal view; D, right fore wing.
Fig. 3 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 3. Aritranis kuro sp. nov. (A, KPM-NK 75838), Buathra nipponica sp. nov. (B, KPM-NK 75746), Cryptus daidaigaster sp. nov. (C, NIAES), Gambrus homonae Sonan, 1930 (D, KPM-NK 76566); Glabridorsum japonicum sp. nov. (E, KPM-NK 75742), Gotra elegans sp. nov. (F, KPM-NK 75822); Hoplocryptus ashoroensis sp. nov. (G, NIAES), Ho. ezoensis sp. nov. (H, KPM-NK 75800), Ho. intermedius sp. nov. (I, KPM-NK 75804), Ho. japonicus sp. nov. (J, KPM-NK 75771), Ho. maculatus sp. nov. (K, KPM-NK 75781), Ho. pini (L, KPM-NK 76579), Ho. toshimensis sp. nov. (M, KPM-NK 75797), Picardiella melanoleuca (Gravenhorst, 1829) (N, KPM-NK 75744) and Trychosis breviterebratus sp. nov. (N, KPM-NK 75758), apex of ovipositor, lateral view.
Fig. 8 in Expression of green fluorescent protein defines a specific population of lamina II excitatory interneurons in the GRP::eGFP mouse
Fig. 8. Glabridorsum japonicum sp. nov. (A, C, E, G, KPM-NK 75742; B, D, F, KPM-NK 75743) ― A, lateral habitus; B, head, mesosoma and metasoma, dorsal view; C, D, mesosoma, lateral view; E, head, frontal view; F, propodeum, dorsal view; G, apical part of right fore wing.
Data - AlphaFold2 Predicts Alternative Conformation Populations in Green Fluorescent Protein Variants
<p><strong>MSAs.zip </strong>Multiple sequences alignments generated by AlphaFold2 structure prediction of 7 engineered GFPs.</p> <p><strong>AF2_models_column_masking.zip </strong>AlphaFold2 models of the alternative conformations of 7 engineered GFPs.</p> <p><strong>MD_trajectories_PyMOL.zip</strong> Molecular dynamics trajectories (PyMOL sessions) of the alternative conformations of 7 engineered GFPs.</p> <p><strong>MD_analysis.zip </strong>Root mean square deviation and per-residue root mean square fluctuations along molecular dynamics simulations of 7 engineered GFPs.</p> <p><strong>rmsd_values.zip</strong> Root mean square deviation relative to crystallographic GFP structure for AlphaFold2 models and molecular dynamics frames (global and central alpha-helix)</p>
FRET efficiency of fluorescent protein pairs with mTurquoise2 as donor
<p>This dataset is was produced in the study of mTurquoise2 paired with a number of spectrally diverse fluorescent proteins as acceptors. For details and see the original paper: <a href="http://www.nature.com/articles/s41598-017-12212-x">https://www.nature.com/articles/s41598-017-12212-x</a></p> <p>These data are reported in table 3 of that paper.</p>
Test data set for macros accompanying the publication Multi-parameter screening method for developing optimized red fluorescent proteins
<p>This a bundle of test data can be used to run the macros accompanying the publication Multi-parameter screening method for developing optimized red fluorescent proteins.</p> <p>These data sets can be used to run the following macros that can be found on GitHub:</p> <ol> <li><a href="https://github.com/molcyto/MC-Ratio-96-wells">https://github.com/molcyto/MC-Ratio-96-wells</a></li> <li><a href="https://github.com/molcyto/MC-Ratio-Petri-dish">https://github.com/molcyto/MC-Ratio-Petri-dish</a></li> <li><a href="https://github.com/molcyto/MC-FLIM-Petri-dish">https://github.com/molcyto/MC-FLIM-Petri-dish</a></li> <li><a href="https://github.com/molcyto/MC-Bleach-96-wells">https://github.com/molcyto/MC-Bleach-96-wells</a></li> <li><a href="https://github.com/molcyto/MC-Scatter5D">https://github.com/molcyto/MC-Scatter5D</a></li> <li><a href="https://github.com/molcyto/MC-FLIM-96-wells">https://github.com/molcyto/MC-FLIM-96-wells</a></li> </ol> <p>Funding:<br> This work was supported by the NWO CW-Echo grant 711.011.018 (M.A.H. and T.W.J.G.), grant 12149 (T.W.J.G.) from the Foundation for Technological Sciences (STW) from the Netherlands</p> <p> </p>
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.