cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6075/j0zp4658
title: CIL:10404, Rattus, multipolar neuron. In Cell Image Library

description: Cultured hippocampal neurons after 23 days in vitro, immunostained for MAP2, a microtubule associated protein localized to dendrites (red), and PSD95, a scaffolding protein concentrated in the postsynaptic density of excitatory synapses, particularly in dendritic spines (green). 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (from S. Halpain) with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch) and PSD95 (from NeuroMab, with Alexa488 conjugated secondary, excitation, 496, emission, 519, Invitrogen). Images were acquired with a Leica DMRA microscope with a 40X lens (HCX PL Fluotar, NA 0.75), Photometrics CoolSnap ES CCD camera and MetaMorph software. The merged image was generated by creating a MetaMorph stack file.
description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; elastic scattering of photons
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Processed;spatialmeasurements
DOI: 10.15468/dl.erfr2s
title: Occurrence Download

description: A dataset containing 8 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Cynanchum chinense"
 ]
}

 The dataset includes 8 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009527-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6069/9j5y-ws41
title: Absence of Flv3 results in metabolic and bioenergetic rearrangements towards mixotrophy in engineered sucrose-excreting Synechocystis sp. PCC6803

description: In the cyanobacterium Synechocystis sp. PCC 6803, the flavodiiron protein Flv3 functions as an alternative electron acceptor from PSI and represents an interesting engineering target for reorganizing the electron and carbon fluxes in the cell. We have shown that the inactivation of Flv3 in engineered sucrose-excreting Synechocystis (S02:Δflv3) triggers sucrose reuptake from the growth medium, and leads to a transition from photoautotrophy to mixotrophy. Such an acclimation maintains optimal growth of the S02:Δflv3 strain through enhanced respiratory metabolism evidenced by extensive but gradual proteomic and metabolomic changes over the course of the nine-day experiment. In the absence of Flv3, a downregulation of photosynthetic light reactions and CO2 assimilation with concurrent upregulation of glycolytic pathways occurred before any differences in sucrose production between S02 and S02:Δflv3 strains were observed. Subsequently, the components of the respiratory pathways showed distinct upregulation in S02:Δflv3, including the plastoquinone reductase complexes NDH-11 and NDH-2, which function at the interphase between glycolytic metabolism and the electron transport pathways, and the terminal respiratory oxidases Cyd and Cox, which direct electrons to O2. Increased oxygen consumption together with lower rates of photosynthetic light reactions generating oxygen led to activation fermentative pathways in S02:Δflv3 as an alternative source of energy for the cells. Our results show that although Synechocystis cannot directly compensate for the lack of Flv3 by other alternative electron acceptors under continuous high light, high CO2 and high osmotic pressure, the cells respond to the increased electron pressure by extensive reorganization of the electron transfer pathways. While glycolytic metabolism is significantly up-regulated to provide energy for the cell, the accumulation of storage compounds and increased respiration serve as indirect electron sinks for photosynthetic electrons that would normally be consumed by the Flv1/Flv3 heterodimer.
DOI: 10.6075/j0sq90c5
title: CIL:10401, Rattus, multipolar neuron. In Cell Image Library

description: Preparation: formaldehyde fixed tissue; detergent permeabilized
Relation to intact cell: dispersed cells in vitro
Item type: recorded image
Imaging mode: fluorescence microscopy; phase contrast microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope; elastic scattering of photons
Visualization methods: primary antibody plus labeled secondary antibody
Processing history: unprocessed raw data
Data qualification: Processed;spatialmeasurements
description: Cultured hippocampal neurons after 23 days in vitro, immunostained for MAP2, a microtubule associated protein localized to dendrites (red), and PSD95, a scaffolding protein concentrated in the postsynaptic density of excitatory synapses, particularly in dendritic spines (green). 

Detailed methods: Embryonic rat hippocampal neurons were prepared as previously described (see Kaech and Banker, 2006, Nat Protoc). Cells were prepared for fluorescent staining as previously described (Withers and Banker, 1998, in Culturing Nerve Cells, MIT Press). Briefly, cells were fixed (4% formaldehyde, 4% sucrose in phosphate buffered saline, pH 7.4), permeabilized with 0.25% Triton and immunostained for MAP2 (from S. Halpain) with d549 conjugated secondary, excitation, 555, emission, 568, Jackson Immunoresearch) and PSD95 (from NeuroMab, with Alexa488 conjugated secondary, excitation, 496, emission, 519, Invitrogen). Images were acquired with a Leica DMRA microscope with a 40X lens (HCX PL Fluotar, NA 0.75), Photometrics CoolSnap ES CCD camera and MetaMorph software. The merged image was generated by creating a MetaMorph stack file.
DOI: 10.6075/j0gh9h5t
title: CIL:10439, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0df6q9n
title: CIL:10438, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes, as seen in this micrograph. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.15468/dl.8zc2fc
title: Occurrence Download

description: A dataset containing 198 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CHN.28_1",
 "TaxonKey is Argentina anserina"
 ]
}

 The dataset includes 198 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009526-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.6075/j0571b4q
title: CIL:10434, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays (CIL:9301). The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes. In this micrograph, large numbers of intermediate filaments are seen; they are evidently very close to the inner surface of the plasma membrane, where they insert into electron-dense desmosomal plagues. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Source of contrast: stain with broad specificity
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0pn94t1
title: CIL:10433, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays. Many of the coils occur perinuclearly, often appearing to be closely associated with the nuclear envelope. The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0pr7v24
title: CIL:10431, Rana catesbeiana, barrier epithelial cell. In Cell Image Library

description: This group of micrographs illustrate the ultrastructural characteristics of the middle layer of the three meningeal layers that cover the central nervous system The arachnoid cells contain abundant intermediate filaments that occupy a substantial volume of the cytoplasm. In some cells the intermediate filaments are organized into numerous coils of relatively uniform size and orientation. The coils appear to stack in loose hexagonal arrays (CIL:9301). The plasma membrane of these cells has many caveolae. Adjacent arachnoid cells are connected by large desmosomes. In this micrograph, large numbers of intermediate filaments are seen; they are evidently very close to the inner surface of the plasma membrane, where they insert into electron-dense desmosomal plagues. Images were recorded using a Philips EM301 TEM at 80 kv. Original glass plates were scanned and digitized using an Epson V750 flatbed scanner with a step size of 15 micrometers. This group of images complement those published in the reference below. Reference: Michaels, JE, Tornheim, PA. Cell Tissue Res. 236:693-697 (1984).
description: Preparation: glutaraldehyde fixed tissue; osmium tetroxide fixed tissue; tissue in plastic embedment
Relation to intact cell: microtome-sectioned tissue
Item type: transmission electron microscopy (TEM)
Imaging mode: illumination by electrons; detection of electrons
Parameter imaged: electron density
Visualization methods: uranyl salt; lead salt; osmium tetroxide
Processing history: unprocessed raw data
DOI: 10.6075/j0ht2nft
title: CIL:10430, Gallus gallus, erythrocyte. In Cell Image Library

description: Nucleated erythrocytes from chicken were spread on water, the dispersed chromatin picked up on carbon-formvar grids, fixed with paraformaldehye, critical point dried and shadowed with platinum. Images were obtained with the Wisconsin high voltage TEM at 1MEV using darkfield illumination. For this micrograph, the grid was tilted to 40 degrees. A similar micrograph tilted to 54 degrees providing a stereo pair with an oblique 3D view of the tangled and irregular chromatin fibers is grouped with this image. The combination of shadowing and darkfield illumination gives a quasi-negative stain effect revealing nucleosomes in some fibers.
description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: spread preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM); darkfield illumination
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j0t152wm
title: CIL:1043, Caenorhabditis elegans, muscle cell. In Cell Image Library

description: Relation to intact cell: whole mounted tissue
Item type: recorded image
Imaging mode: fluorescence microscopy
Parameter imaged: fluorescence emission
Source of contrast: distribution of epitope
Visualization methods: phalloidin
Processing history: unprocessed raw data
description: C. elegans muscle age is a data set of fluorescence 20X microscopy images of C. elegans nematodes stained with phalloidin to visualize actin in muscles at different ages (1,2,4, and 8). Note that the data sets for each age can be found by searching for a featured image from each set: CIL 1005, 1057, 1105, and 1265, respectively.
description: The purpose of the dataset C. elegans muscle aging is to deduce the age of the nemathode based on images of muscles. Images of C. elegans were taken at different chronological ages. This image is part of the day 1 data set. Note that the morphological and chronological ages are not fully correlated due to the variability among individuals even though the individuals are genetically identical. The source for the dataset is Laboratory of Genetics/NIA/NIH.
DOI: 10.6075/j0bz6567
title: CIL:10426, Gallus gallus, erythrocyte. In Cell Image Library

description: Nucleated erythrocytes from chicken were spread on water, the dispersed chromatin picked up on carbon-formvar grids, fixed with paraformaldehye, critical point dried and shadowed with platinum. Images were obtained with the Wisconsin high voltage TEM at 1MEV using darkfield illumination. For this micrograph, the grid was tilted to 55 degrees. A similar micrograph tilted to 44 degrees providing a stereo pair with an oblique 3D view of the tangled and irregular chromatin fibers is grouped with this image. The combination of shadowing and darkfield illumination gives a quasi-negative stain effect revealing nucleosomes in some fibers.
description: Preparation: formaldehyde fixed tissue; critical_point dried specimen
Relation to intact cell: spread preparation
Item type: film
Imaging mode: transmission electron microscopy (TEM); darkfield illumination
Parameter imaged: electron density
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
DOI: 10.6075/j03j3bjb
title: CIL:47514, Staphylococcus aureus, neutrophil, endothelial cell. In Cell Image Library

description: Mice were anesthetized with ketamine/xylazine, and then subcutaneous tissue on a dorsal flap was exteriorized. GFP labelled S. aureus beads were inserted. Antibodies were injected into the vasculature to label neutrophils (red) and endothelial cells (blue)
description: Visualization of neutrophil recruitment in capillaries proximal to S. aureus beads. (Figure 3 - A4 block)
description: Relation to intact cell: intact cells-in vivo imaging
Item type: recorded image
Imaging mode: spinning disk confocal microscopy
Processing history: Converted from volocity to .avi
DOI: 10.6075/j0jd4wfn
title: CIL: 53521, Homo sapiens, HeLa. In Cell Image Library

description: Visualization methods: confocal microscopy
description: Kinome Atlas documented representative images for 456 kinases expressed in HeLa cells, and visualized by immunofluorescence staining of the epitope tag. Nuclei were stained with DAPI. Two representative views from confocal microscopy were collected for each kinase. Also, organelle markers were co-stained for some kinases to indicate specific localization.
description: AGC family: The human kinome comprises 538 kinases playing essential cellular functions by catalyzing protein phosphorylations. Systematic annotation of subcellular spatial distribution of the kinome greatly facilitates investigation of normal and disease mechanisms. Here, we present Kinome Atlas (KA), an image-based map of the kinome annotated to 10 compartments of the cell. 456 epitope-tagged kinases, representing 85% of the human kinome, were expressed in HeLa cells and imaged by immunofluorescent microscopy under a unified condition. KA revealed kinase family-enriched subcellular localizations, and discovered a collection of new kinase localizations at mitochondria, plasma membrane, extracellular space, and other unique structures. This resource provides the first snapshot of the kinome under a unified condition, and is a key step toward comprehensive understanding of the spatial and temporal dynamics of the kinome in physiological and disease states.
DOI: 10.6075/j0z89bgq
title: CIL:6268, Oryctolagus cuniculus, skeletal muscle cell. In Cell Image Library

description: Preparation: unfixed tissue; freeze_fracture/freeze_etch; whole mounted tissue
Relation to intact cell: isolated subcellular component
Item type: recorded image
Imaging mode: transmission electron microscopy (TEM); wide-field detection; widefield illumination; illumination by electrons; detection of electrons
Parameter imaged: electron density; elevation
Source of contrast: differences in deposition of metal shadow
Visualization methods: shadowing and plating
Processing history: unprocessed raw data
description: Rabbit psoas skeletal muscle fibers were blended in the presence of 5 mM MgATP to dissociate thick and thin filaments. The medium was then gently replaced with 0.3M KCl to dissociate thick filaments. Dissociated filaments were adsorbed onto mica flakes (Heuser JE, J Mol Biol. 1983 Sep 5;169(1):155-95), quick-frozen by contact with a liquid helium- cooled copper block in a Heuser-type cryopress, and freeze-etched in a Balzers 400 freeze fracture machine. The sample was then rotary-replicated with Pt-C at 11 degrees and visualized in a JEOL transmission electron microscope operated at 100 kev.

This image was recorded on Kodak 4489 film at 80,000x magnification. Stereo pairs were taken at +5 and -5 degrees. Films were scanned with a 20 micrometer pixel spacing on a Nikon Coolscan 9000ED scanner.

Stereo pair with CIL:6269.