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Carl Zeiss gfp expression
<t>cyp-36A1</t> expression in multiple tissues rescues the egg-laying phenotype of cyp-36A1(lf); egl-9(lf) . ( A–H ) Distribution of stages of eggs laid by adult hermaphrodites of the indicated genotypes. All strains contained the agIs219 ( P T24B8.5 <t>::gfp</t> ) transgene. ( A ) Stages of eggs laid by wild-type animals. ( B ) egl-9(sa307) animals laid later stage eggs than wild type (p
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Images

1) Product Images from "Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor"

Article Title: Hypoxia-inducible factor cell non-autonomously regulates C. elegans stress responses and behavior via a nuclear receptor

Journal: eLife

doi: 10.7554/eLife.36828

cyp-36A1 expression in multiple tissues rescues the egg-laying phenotype of cyp-36A1(lf); egl-9(lf) . ( A–H ) Distribution of stages of eggs laid by adult hermaphrodites of the indicated genotypes. All strains contained the agIs219 ( P T24B8.5 ::gfp ) transgene. ( A ) Stages of eggs laid by wild-type animals. ( B ) egl-9(sa307) animals laid later stage eggs than wild type (p
Figure Legend Snippet: cyp-36A1 expression in multiple tissues rescues the egg-laying phenotype of cyp-36A1(lf); egl-9(lf) . ( A–H ) Distribution of stages of eggs laid by adult hermaphrodites of the indicated genotypes. All strains contained the agIs219 ( P T24B8.5 ::gfp ) transgene. ( A ) Stages of eggs laid by wild-type animals. ( B ) egl-9(sa307) animals laid later stage eggs than wild type (p

Techniques Used: Expressing

cyp-36A1 is expressed in many tissues. ( A–D ) Paired fluorescent (left in each panel) and Nomarski (right in each panel) micrographs showing expression of a transcriptional P cyp-36A1 ::gfp reporter ( nIs682 ) in an adult worm. Expression was observed in the head ( A ), midbody ( B and C ), and tail ( D ), including in neurons, body-wall muscle, vulval muscle, intestine, and hypoderm, as indicated. Scale bars, 20 μm.
Figure Legend Snippet: cyp-36A1 is expressed in many tissues. ( A–D ) Paired fluorescent (left in each panel) and Nomarski (right in each panel) micrographs showing expression of a transcriptional P cyp-36A1 ::gfp reporter ( nIs682 ) in an adult worm. Expression was observed in the head ( A ), midbody ( B and C ), and tail ( D ), including in neurons, body-wall muscle, vulval muscle, intestine, and hypoderm, as indicated. Scale bars, 20 μm.

Techniques Used: Expressing

2) Product Images from "High fidelity electrophysiological, morphological, and transcriptomic cell characterization using a refined Patch-seq protocol"

Article Title: High fidelity electrophysiological, morphological, and transcriptomic cell characterization using a refined Patch-seq protocol

Journal: bioRxiv

doi: 10.1101/2020.11.04.369082

Example biocytin recovery and morphology calls. ( A ) is a 20x brightfield image of a coronal slice from a Sst-Cre line containing biocytin fills from four Patch-seq recordings. ( B-D ) are 63x MIP images from the regions identified in ( A ) and their subsequent morphology outcome. ( B ) contains failed insufficient axon, left, and medium quality, right, fills; ( C ) is a failed fill, and ( D ) is a high-quality fill with corresponding morphological reconstruction with dendrites in red and axon in blue.
Figure Legend Snippet: Example biocytin recovery and morphology calls. ( A ) is a 20x brightfield image of a coronal slice from a Sst-Cre line containing biocytin fills from four Patch-seq recordings. ( B-D ) are 63x MIP images from the regions identified in ( A ) and their subsequent morphology outcome. ( B ) contains failed insufficient axon, left, and medium quality, right, fills; ( C ) is a failed fill, and ( D ) is a high-quality fill with corresponding morphological reconstruction with dendrites in red and axon in blue.

Techniques Used:

3) Product Images from "Semisynthetic fluorescent pH sensors for imaging exocytosis and endocytosis"

Article Title: Semisynthetic fluorescent pH sensors for imaging exocytosis and endocytosis

Journal: Nature Communications

doi: 10.1038/s41467-017-01752-5

Design and characterization of semisynthetic fluorescent reporters for exocytosis. a Three protein labeling strategies for imaging exocytosis. Cartoons depicting vesicles expressing pH-sensitive fluorescent protein, such as SEP or pHuji, fused to a SV protein (i) or SNAP-tag enzyme fused to an SV protein and labeled with a pH-sensitive organic fluorophore (ii) and labeling of endogenous SV proteins with an antibody conjugated to a pH-sensitive dye (iii). b Chemical structures of Fl (1), CFl (2), and VO (3). c Fl and CFl respond differently to pH. Fluorescein undergoes noncooperative protonation from the dianion (1 2− ) to the monoanion (1 − ), whereas carbofluorescein undergoes cooperative protonation from the highly colored dianion (2 2− ) to a colorless lactone form (2lactone). d Image of cuvettes containing compounds 1 or 2 (5 μM) at pH 5.6 and pH 7.4. e Plot of fluorescence vs. pH for compounds 1, 2, and 3. f Chemical structure of CFl–SNAP-tag ligand (4) and VO–SNAP-tag ligand (5). g PAGE of SNAP-tag protein labeled with compound 4 and visualized by Coomassie staining or by fluorescence (indicated by arrows). h Plot of fluorescence vs. pH for 4–SNAP-tag conjugate. p K a = 7.3 and η H = 1.2. i Absolute absorbance of 4–SNAP-tag conjugate (~3 µM) at pH 7.4 (magenta) and pH 5.6 (black). Error bars represent s.d. for 4 experiments each
Figure Legend Snippet: Design and characterization of semisynthetic fluorescent reporters for exocytosis. a Three protein labeling strategies for imaging exocytosis. Cartoons depicting vesicles expressing pH-sensitive fluorescent protein, such as SEP or pHuji, fused to a SV protein (i) or SNAP-tag enzyme fused to an SV protein and labeled with a pH-sensitive organic fluorophore (ii) and labeling of endogenous SV proteins with an antibody conjugated to a pH-sensitive dye (iii). b Chemical structures of Fl (1), CFl (2), and VO (3). c Fl and CFl respond differently to pH. Fluorescein undergoes noncooperative protonation from the dianion (1 2− ) to the monoanion (1 − ), whereas carbofluorescein undergoes cooperative protonation from the highly colored dianion (2 2− ) to a colorless lactone form (2lactone). d Image of cuvettes containing compounds 1 or 2 (5 μM) at pH 5.6 and pH 7.4. e Plot of fluorescence vs. pH for compounds 1, 2, and 3. f Chemical structure of CFl–SNAP-tag ligand (4) and VO–SNAP-tag ligand (5). g PAGE of SNAP-tag protein labeled with compound 4 and visualized by Coomassie staining or by fluorescence (indicated by arrows). h Plot of fluorescence vs. pH for 4–SNAP-tag conjugate. p K a = 7.3 and η H = 1.2. i Absolute absorbance of 4–SNAP-tag conjugate (~3 µM) at pH 7.4 (magenta) and pH 5.6 (black). Error bars represent s.d. for 4 experiments each

Techniques Used: Labeling, Imaging, Expressing, Fluorescence, Polyacrylamide Gel Electrophoresis, Staining

4) Product Images from "A simple and highly efficient Agrobacterium-mediated transformation protocol for Setaria viridis"

Article Title: A simple and highly efficient Agrobacterium-mediated transformation protocol for Setaria viridis

Journal: Biotechnology Reports

doi: 10.1016/j.btre.2015.02.002

Agrobacterium tumefaciens -mediated transformation of Setaria viridis . (a) embryogenic callus after 5 weeks in CIM medium (bar = 2 mm). (b) translucent embryogenic callus most suitable for transformation (arrow heads, bar = 0.5 mm). (c) PCR analysis of the transgenic plants with gfp specific primer (NT: non-transgenic plant, lanes 1–11 transgenic plants, M: molecular weight marker – 100 bp DNA Ladder). (d) Transgenic plant expressing GUS (right) and non-transgenic (left). (e) Transgenic T1 seeds expressing GFP (top) and T 1 seedlings expressing GFP (bottom). (f) Regenerated transgenic plantlet in hygromicin-containing selective MS medium (arrow head).
Figure Legend Snippet: Agrobacterium tumefaciens -mediated transformation of Setaria viridis . (a) embryogenic callus after 5 weeks in CIM medium (bar = 2 mm). (b) translucent embryogenic callus most suitable for transformation (arrow heads, bar = 0.5 mm). (c) PCR analysis of the transgenic plants with gfp specific primer (NT: non-transgenic plant, lanes 1–11 transgenic plants, M: molecular weight marker – 100 bp DNA Ladder). (d) Transgenic plant expressing GUS (right) and non-transgenic (left). (e) Transgenic T1 seeds expressing GFP (top) and T 1 seedlings expressing GFP (bottom). (f) Regenerated transgenic plantlet in hygromicin-containing selective MS medium (arrow head).

Techniques Used: Transformation Assay, Polymerase Chain Reaction, Transgenic Assay, Molecular Weight, Marker, Expressing, Mass Spectrometry

5) Product Images from "Bacillus anthracis chain length, a virulence determinant, is regulated by a transmembrane Ser/Thr protein kinase PrkC"

Article Title: Bacillus anthracis chain length, a virulence determinant, is regulated by a transmembrane Ser/Thr protein kinase PrkC

Journal: bioRxiv

doi: 10.1101/2020.03.15.992834

Effect of prkC disruption on chaining morphotype during different phases of bacterial growth. (A) Growth kinetics of BAS WT. BAS WT strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (B) Growth kinetics of BAS Δ prkC . BAS Δ prkC strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (C) Phase contrast images of BAS WT and BAS Δ prkC strains at different phases of bacterial growth cycle. Cells were grown at 37°C in LB broth and 1 ml sample was harvested at time points indicated in Fig. 2A and Fig. 2B . Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm.
Figure Legend Snippet: Effect of prkC disruption on chaining morphotype during different phases of bacterial growth. (A) Growth kinetics of BAS WT. BAS WT strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (B) Growth kinetics of BAS Δ prkC . BAS Δ prkC strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (C) Phase contrast images of BAS WT and BAS Δ prkC strains at different phases of bacterial growth cycle. Cells were grown at 37°C in LB broth and 1 ml sample was harvested at time points indicated in Fig. 2A and Fig. 2B . Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm.

Techniques Used: Standard Deviation, Microscopy

prkC disruption results in bacteria with short chain length. (A) Photograph of culture sediments in microcentrifuge tubes after standing incubation (9 hr) at room temperature of BAS WT (left) and BAS Δ prkC (right) grown in LB media. (B) Phase contrast images of BAS WT, BAS Δ prkC and BAS Δ prkC :: prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and 1 ml sample was taken from cultures in mid-log phase. Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm. (C) Scanning electron microscopy of BAS WT and BAS Δ prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and harvested in mid-log phase. These were then washed with 0.1 M sodium phosphate buffer and fixed with Karnovasky’s fixative followed by 1% osmium tetroxide. A critical point drying technique was used for drying the samples followed by gold coating of 10 nm using an aluminium stubs coated with agar sputter. Cells were visualized under Zeiss Evo LS15. Scale bar represent 2 μm, magnification-5000X.
Figure Legend Snippet: prkC disruption results in bacteria with short chain length. (A) Photograph of culture sediments in microcentrifuge tubes after standing incubation (9 hr) at room temperature of BAS WT (left) and BAS Δ prkC (right) grown in LB media. (B) Phase contrast images of BAS WT, BAS Δ prkC and BAS Δ prkC :: prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and 1 ml sample was taken from cultures in mid-log phase. Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm. (C) Scanning electron microscopy of BAS WT and BAS Δ prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and harvested in mid-log phase. These were then washed with 0.1 M sodium phosphate buffer and fixed with Karnovasky’s fixative followed by 1% osmium tetroxide. A critical point drying technique was used for drying the samples followed by gold coating of 10 nm using an aluminium stubs coated with agar sputter. Cells were visualized under Zeiss Evo LS15. Scale bar represent 2 μm, magnification-5000X.

Techniques Used: Incubation, Microscopy, Electron Microscopy

6) Product Images from "Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons"

Article Title: Toward an integrated classification of neuronal cell types: morphoelectric and transcriptomic characterization of individual GABAergic cortical neurons

Journal: bioRxiv

doi: 10.1101/2020.02.03.932244

Data pipeline schematic. (A) Each cell underwent standardized collection of electrophysiology data, followed by a series of processing and quality control steps in parallel for each modality. Transcriptomic analysis included extraction and reverse transcription of the cell’s nuclear and cytosolic mRNA, followed by cDNA amplification, sequencing and evaluation of data quality based on normalized summed expression of “on”-type marker genes (NMS) adapted from the single-cell quality control measures in ( Tripathy et al., 2018 ). Electrophysiological analysis included cell and sweep-level quality control gates, and automated extraction of feature vectors. Electrophysiology slices were stained, mounted onto coverslips, imaged at 20x and mapped to the Allen Mouse Common Coordinate Framework (CCF). QC-Qualified cells had an NMS > 0.4, passed electrophysiology quality control and feature extraction and had a confirmed soma location in primary visual cortex (VISp). A subset of cells with high-quality cell fills were further processed for morphological reconstruction. (B) Schematic of reference data set and mapping tree. (C) Assignment of t-types to cells assayed via Patch-seq recordings. QC-qualified cells from (A) were mapped on the reference dataset obtained in (B) using two different mapping algorithms (see (D) and (E)). (D) Schematic illustrating mapping procedure using the reference taxonomy tree. (E) Schematic illustrating mapping using a neural network classifier. (F) Calculation of reference mapping confusion matrix. The reference dissociated cells from ( Tasic et al., 2018 ) were mapped to the reference taxonomy tree using the same method in (D), and the mapping probability matrix of those cells was computed. This probability matrix and the clustering results from ( Tasic et al., 2018 ) of those dissociated cells were used as inputs to compute the reference confusion matrix. (G) Schematic illustrating the determination of mapping quality to each cell assayed via Patch-seq recordings.
Figure Legend Snippet: Data pipeline schematic. (A) Each cell underwent standardized collection of electrophysiology data, followed by a series of processing and quality control steps in parallel for each modality. Transcriptomic analysis included extraction and reverse transcription of the cell’s nuclear and cytosolic mRNA, followed by cDNA amplification, sequencing and evaluation of data quality based on normalized summed expression of “on”-type marker genes (NMS) adapted from the single-cell quality control measures in ( Tripathy et al., 2018 ). Electrophysiological analysis included cell and sweep-level quality control gates, and automated extraction of feature vectors. Electrophysiology slices were stained, mounted onto coverslips, imaged at 20x and mapped to the Allen Mouse Common Coordinate Framework (CCF). QC-Qualified cells had an NMS > 0.4, passed electrophysiology quality control and feature extraction and had a confirmed soma location in primary visual cortex (VISp). A subset of cells with high-quality cell fills were further processed for morphological reconstruction. (B) Schematic of reference data set and mapping tree. (C) Assignment of t-types to cells assayed via Patch-seq recordings. QC-qualified cells from (A) were mapped on the reference dataset obtained in (B) using two different mapping algorithms (see (D) and (E)). (D) Schematic illustrating mapping procedure using the reference taxonomy tree. (E) Schematic illustrating mapping using a neural network classifier. (F) Calculation of reference mapping confusion matrix. The reference dissociated cells from ( Tasic et al., 2018 ) were mapped to the reference taxonomy tree using the same method in (D), and the mapping probability matrix of those cells was computed. This probability matrix and the clustering results from ( Tasic et al., 2018 ) of those dissociated cells were used as inputs to compute the reference confusion matrix. (G) Schematic illustrating the determination of mapping quality to each cell assayed via Patch-seq recordings.

Techniques Used: Amplification, Sequencing, Expressing, Marker, Staining

7) Product Images from "The Rat Mammary Gland as a Novel Site of Expression of Melanin-Concentrating Hormone Receptor 1 mRNA and Its Protein Immunoreactivity"

Article Title: The Rat Mammary Gland as a Novel Site of Expression of Melanin-Concentrating Hormone Receptor 1 mRNA and Its Protein Immunoreactivity

Journal: Frontiers in Endocrinology

doi: 10.3389/fendo.2020.00463

MCHR1 immunoreactivity in the skin and parenchyma of the rat mammary gland tissue. Wide field fluorescence photomicrographs of sagittal mammary gland slices from diestrus and PPD19 rats ( n = 3/group) submitted to indirect immunofluorescence for MCHR1 (red) and counterstained with DAPI nuclear stain (blue). (A,B) In the skin of mammary gland the MCHR1-ir cells are found in the epidermis, distributed all over the basal, spinous, granular layers, and cornified layer. Some of the accessory epidermal structures of the skin were labeled, such as the fat cells of the sebaceous gland and cells of the hair follicle. (A') The undeveloped parenchyma on diestrus phase shows few or absence immunolabeling for MCHR1. (B') The parenchyma on PPD19 display MCHR-ir cells bordering and into the luminal part of the acini and ducts. The MCHR1-ir cells are indicated by white arrowheads. a, acini ; ep, epidermis; de, dermis; hf, hair follicle; d, duct. Scale bar: 50 μm.
Figure Legend Snippet: MCHR1 immunoreactivity in the skin and parenchyma of the rat mammary gland tissue. Wide field fluorescence photomicrographs of sagittal mammary gland slices from diestrus and PPD19 rats ( n = 3/group) submitted to indirect immunofluorescence for MCHR1 (red) and counterstained with DAPI nuclear stain (blue). (A,B) In the skin of mammary gland the MCHR1-ir cells are found in the epidermis, distributed all over the basal, spinous, granular layers, and cornified layer. Some of the accessory epidermal structures of the skin were labeled, such as the fat cells of the sebaceous gland and cells of the hair follicle. (A') The undeveloped parenchyma on diestrus phase shows few or absence immunolabeling for MCHR1. (B') The parenchyma on PPD19 display MCHR-ir cells bordering and into the luminal part of the acini and ducts. The MCHR1-ir cells are indicated by white arrowheads. a, acini ; ep, epidermis; de, dermis; hf, hair follicle; d, duct. Scale bar: 50 μm.

Techniques Used: Fluorescence, Immunofluorescence, Staining, Labeling, Immunolabeling

MCHR1 immunoreactivity in the rat mammary gland. Wide field fluorescence photomicrographs of sagittal mammary gland slices from diestrus and lactating rats ( n = 3/group) submitted to indirect immunofluorescence for MCHR1 (red) and counterstained with DAPI nuclear stain (blue). (A) The mammary gland of diestrus, a tissue that is not totally differentiated as a lactating tissue, presents few MCHR1-ir cells. (A') Higher magnification of the square area in (A) showing few MCHR1-ir cells located mainly in islands of undifferentiated parenchyma of mammary gland tissue surrounded by adipose tissue. (B–D) Along the different time points of the lactation, there is an evident effect of lactation in the presence and location of MCHR1-ir cells in the rat mammary gland tissue. (B'–D') Higher magnification of the square areas in (A–D) . There is an increasing of MCHR-ir cells bordering and into the luminal part of the acini at PPD19 (D') when compared with the (B') PPD5 and (C') PPD12, which is similar with qPCR and Western blotting data. The MCHR1-ir cells are indicated by white arrowheads. Scale bars: 50 μm (A–D) , 20 μm (A'–D') .
Figure Legend Snippet: MCHR1 immunoreactivity in the rat mammary gland. Wide field fluorescence photomicrographs of sagittal mammary gland slices from diestrus and lactating rats ( n = 3/group) submitted to indirect immunofluorescence for MCHR1 (red) and counterstained with DAPI nuclear stain (blue). (A) The mammary gland of diestrus, a tissue that is not totally differentiated as a lactating tissue, presents few MCHR1-ir cells. (A') Higher magnification of the square area in (A) showing few MCHR1-ir cells located mainly in islands of undifferentiated parenchyma of mammary gland tissue surrounded by adipose tissue. (B–D) Along the different time points of the lactation, there is an evident effect of lactation in the presence and location of MCHR1-ir cells in the rat mammary gland tissue. (B'–D') Higher magnification of the square areas in (A–D) . There is an increasing of MCHR-ir cells bordering and into the luminal part of the acini at PPD19 (D') when compared with the (B') PPD5 and (C') PPD12, which is similar with qPCR and Western blotting data. The MCHR1-ir cells are indicated by white arrowheads. Scale bars: 50 μm (A–D) , 20 μm (A'–D') .

Techniques Used: Fluorescence, Immunofluorescence, Staining, Real-time Polymerase Chain Reaction, Western Blot

8) Product Images from "Filopodia formation and endosome clustering induced by mutant plus-end–directed myosin VI"

Article Title: Filopodia formation and endosome clustering induced by mutant plus-end–directed myosin VI

Journal: Proceedings of the National Academy of Sciences of the United States of America

doi: 10.1073/pnas.1616941114

Comparison of the role of actin-regulating proteins in formation of filopodia by MYO6+ and MYO10. ( A ) Widefield fluorescence microscopy images of cells either mock treated or transfected with siRNA against either ARP3, DIAPH3, or N-WASP, transfected with
Figure Legend Snippet: Comparison of the role of actin-regulating proteins in formation of filopodia by MYO6+ and MYO10. ( A ) Widefield fluorescence microscopy images of cells either mock treated or transfected with siRNA against either ARP3, DIAPH3, or N-WASP, transfected with

Techniques Used: Fluorescence, Microscopy, Transfection

MYO6+ sequesters MYO6 binding partners into filopodia. Widefield images of HeLa cells expressing GFP-MYO6+ fixed and stained with antibodies to ( A ) TOM1 ( Insets shown are 5× magnification); ( B ) DOCK7, TAX1BP1, or DAB2; and ( C ) optineurin or NDP52.
Figure Legend Snippet: MYO6+ sequesters MYO6 binding partners into filopodia. Widefield images of HeLa cells expressing GFP-MYO6+ fixed and stained with antibodies to ( A ) TOM1 ( Insets shown are 5× magnification); ( B ) DOCK7, TAX1BP1, or DAB2; and ( C ) optineurin or NDP52.

Techniques Used: Binding Assay, Expressing, Staining

9) Product Images from "High fidelity electrophysiological, morphological, and transcriptomic cell characterization using a refined Patch-seq protocol"

Article Title: High fidelity electrophysiological, morphological, and transcriptomic cell characterization using a refined Patch-seq protocol

Journal: bioRxiv

doi: 10.1101/2020.11.04.369082

The optimized Patch-seq protocol consists of electrophysiological recording followed by nucleus retrieval and extraction. A schematic of the three major stages of the Patch-seq protocol: ( A ) recording, ( B ) nucleus retrieval, and ( C ) nucleus extraction. Histograms represent the binned time spent for ( D ) recording (N=6,720), ( E ) nucleus retrieval (N=5,692), and ( F ) nucleus extraction (N=5,442). ( G ) Time series of high-resolution images showing the gradual pipette retraction with subsequent nucleus extraction. In ( G1 ), the red line denotes outline of soma and the last panel is the fill of the soma and processes visualized by Alexa-488. Yellow asterisk identifies the nucleus as it is extracted from the soma. Blue caret identifies the somatic membrane as it is stretched with the extraction of the nucleus. ( H ) is the time plot of steady state resistance, as measured from the test pulse, during the nucleus extraction phase for the cell in (G) with numbers corresponding to brightfield image.
Figure Legend Snippet: The optimized Patch-seq protocol consists of electrophysiological recording followed by nucleus retrieval and extraction. A schematic of the three major stages of the Patch-seq protocol: ( A ) recording, ( B ) nucleus retrieval, and ( C ) nucleus extraction. Histograms represent the binned time spent for ( D ) recording (N=6,720), ( E ) nucleus retrieval (N=5,692), and ( F ) nucleus extraction (N=5,442). ( G ) Time series of high-resolution images showing the gradual pipette retraction with subsequent nucleus extraction. In ( G1 ), the red line denotes outline of soma and the last panel is the fill of the soma and processes visualized by Alexa-488. Yellow asterisk identifies the nucleus as it is extracted from the soma. Blue caret identifies the somatic membrane as it is stretched with the extraction of the nucleus. ( H ) is the time plot of steady state resistance, as measured from the test pulse, during the nucleus extraction phase for the cell in (G) with numbers corresponding to brightfield image.

Techniques Used: Transferring

Example biocytin recovery and morphology calls. ( A ) is a 20x brightfield image of a coronal slice from a Sst-Cre line containing biocytin fills from four Patch-seq recordings. ( B-D ) are 63x MIP images from the regions identified in ( A ) and their subsequent morphology outcome. ( B ) contains failed insufficient axon, left, and medium quality, right, fills; ( C ) is a failed fill, and ( D ) is a high-quality fill with corresponding morphological reconstruction with dendrites in red and axon in blue.
Figure Legend Snippet: Example biocytin recovery and morphology calls. ( A ) is a 20x brightfield image of a coronal slice from a Sst-Cre line containing biocytin fills from four Patch-seq recordings. ( B-D ) are 63x MIP images from the regions identified in ( A ) and their subsequent morphology outcome. ( B ) contains failed insufficient axon, left, and medium quality, right, fills; ( C ) is a failed fill, and ( D ) is a high-quality fill with corresponding morphological reconstruction with dendrites in red and axon in blue.

Techniques Used:

10) Product Images from "An Erg11 lanosterol 14-α-demethylase-Arv1 complex is required for Candida albicans virulence"

Article Title: An Erg11 lanosterol 14-α-demethylase-Arv1 complex is required for Candida albicans virulence

Journal: PLoS ONE

doi: 10.1371/journal.pone.0235746

Scarv1 cells expressing ScArv1 C27A accumulates cytosolic ER membrane structures. S . cerevisiae cells were grown in the appropriate plasmid selection medium. Cells were transformed with YCplac111-RTN2-GFP (RTN2 under its own promoter in CEN/ARS LEU2 vector). For microscopy studies, cells were diluted to approximately OD 600nm 0.15. Cells were imaged using a Zeiss AxioImager.Z2 epifluorescence upright microscope with a 100X Plan-Apochromatic 1.4 numerical aperture objective lens. An increase in ER membrane fluorescence at medial (B) or cortical optical sections (D) were manually detected as described in Materials and Methods. (E) Percentage of cells displaying cytosolic ER membranes. (F) Percentage of cells displaying peripheral ER aggregates. 300–500 cells were counted in 3 individual experiments. Arrows in panels B D point out cytosolic ER membranes and peripheral ER aggregates, respectively. White bar represents 10 um. * p ≤ 0 . 01 ; ** p ≤ 0 . 001 ; *** p ≤ 0 . 0001 .
Figure Legend Snippet: Scarv1 cells expressing ScArv1 C27A accumulates cytosolic ER membrane structures. S . cerevisiae cells were grown in the appropriate plasmid selection medium. Cells were transformed with YCplac111-RTN2-GFP (RTN2 under its own promoter in CEN/ARS LEU2 vector). For microscopy studies, cells were diluted to approximately OD 600nm 0.15. Cells were imaged using a Zeiss AxioImager.Z2 epifluorescence upright microscope with a 100X Plan-Apochromatic 1.4 numerical aperture objective lens. An increase in ER membrane fluorescence at medial (B) or cortical optical sections (D) were manually detected as described in Materials and Methods. (E) Percentage of cells displaying cytosolic ER membranes. (F) Percentage of cells displaying peripheral ER aggregates. 300–500 cells were counted in 3 individual experiments. Arrows in panels B D point out cytosolic ER membranes and peripheral ER aggregates, respectively. White bar represents 10 um. * p ≤ 0 . 01 ; ** p ≤ 0 . 001 ; *** p ≤ 0 . 0001 .

Techniques Used: Expressing, Plasmid Preparation, Selection, Transformation Assay, Microscopy, Fluorescence

11) Product Images from "A simple and highly efficient Agrobacterium-mediated transformation protocol for Setaria viridis "

Article Title: A simple and highly efficient Agrobacterium-mediated transformation protocol for Setaria viridis

Journal: Biotechnology Reports

doi: 10.1016/j.btre.2015.02.002

Agrobacterium tumefaciens -mediated transformation of Setaria viridis . (a) embryogenic callus after 5 weeks in CIM medium (bar = 2 mm). (b) translucent embryogenic callus most suitable for transformation (arrow heads, bar = 0.5 mm). (c) PCR analysis of the transgenic plants with gfp specific primer (NT: non-transgenic plant, lanes 1–11 transgenic plants, M: molecular weight marker – 100 bp DNA Ladder). (d) Transgenic plant expressing GUS (right) and non-transgenic (left). (e) Transgenic T1 seeds expressing GFP (top) and T 1 seedlings expressing GFP (bottom). (f) Regenerated transgenic plantlet in hygromicin-containing selective MS medium (arrow head).
Figure Legend Snippet: Agrobacterium tumefaciens -mediated transformation of Setaria viridis . (a) embryogenic callus after 5 weeks in CIM medium (bar = 2 mm). (b) translucent embryogenic callus most suitable for transformation (arrow heads, bar = 0.5 mm). (c) PCR analysis of the transgenic plants with gfp specific primer (NT: non-transgenic plant, lanes 1–11 transgenic plants, M: molecular weight marker – 100 bp DNA Ladder). (d) Transgenic plant expressing GUS (right) and non-transgenic (left). (e) Transgenic T1 seeds expressing GFP (top) and T 1 seedlings expressing GFP (bottom). (f) Regenerated transgenic plantlet in hygromicin-containing selective MS medium (arrow head).

Techniques Used: Transformation Assay, Polymerase Chain Reaction, Transgenic Assay, Molecular Weight, Marker, Expressing, Mass Spectrometry

12) Product Images from "A simple and highly efficient Agrobacterium-mediated transformation protocol for Setaria viridis "

Article Title: A simple and highly efficient Agrobacterium-mediated transformation protocol for Setaria viridis

Journal: Biotechnology Reports

doi: 10.1016/j.btre.2015.02.002

Agrobacterium tumefaciens -mediated transformation of Setaria viridis . (a) embryogenic callus after 5 weeks in CIM medium (bar = 2 mm). (b) translucent embryogenic callus most suitable for transformation (arrow heads, bar = 0.5 mm). (c) PCR analysis of the transgenic plants with gfp specific primer (NT: non-transgenic plant, lanes 1–11 transgenic plants, M: molecular weight marker – 100 bp DNA Ladder). (d) Transgenic plant expressing GUS (right) and non-transgenic (left). (e) Transgenic T1 seeds expressing GFP (top) and T 1 seedlings expressing GFP (bottom). (f) Regenerated transgenic plantlet in hygromicin-containing selective MS medium (arrow head).
Figure Legend Snippet: Agrobacterium tumefaciens -mediated transformation of Setaria viridis . (a) embryogenic callus after 5 weeks in CIM medium (bar = 2 mm). (b) translucent embryogenic callus most suitable for transformation (arrow heads, bar = 0.5 mm). (c) PCR analysis of the transgenic plants with gfp specific primer (NT: non-transgenic plant, lanes 1–11 transgenic plants, M: molecular weight marker – 100 bp DNA Ladder). (d) Transgenic plant expressing GUS (right) and non-transgenic (left). (e) Transgenic T1 seeds expressing GFP (top) and T 1 seedlings expressing GFP (bottom). (f) Regenerated transgenic plantlet in hygromicin-containing selective MS medium (arrow head).

Techniques Used: Transformation Assay, Polymerase Chain Reaction, Transgenic Assay, Molecular Weight, Marker, Expressing, Mass Spectrometry

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Confocal Microscopy:

Article Title: Targeted Changes of the Cell Wall Proteome Influence Candida albicans Ability to Form Single- and Multi-strain Biofilms
Article Snippet: .. Confocal microscopy was then performed on the recovered plastic substrates, using a Zeiss LSM 700 laser scanning confocal microscope on an upright Axio Imager Z2 stand, using a Zeiss W-nACHROPLAN 40X/0.75 working distance 2.1 mm objective; z-stacks of the biofilms were obtained using the blue and green lasers, for the whole biofilm thickness. .. Z-stacks were then analyzed using Volocity software to acquire the volume occupied by the cells in the green channel (overexpression mutant, expressing GFP) and by the cells in the blue channel (control strain, expressing BFP).

Microscopy:

Article Title: Targeted Changes of the Cell Wall Proteome Influence Candida albicans Ability to Form Single- and Multi-strain Biofilms
Article Snippet: .. Confocal microscopy was then performed on the recovered plastic substrates, using a Zeiss LSM 700 laser scanning confocal microscope on an upright Axio Imager Z2 stand, using a Zeiss W-nACHROPLAN 40X/0.75 working distance 2.1 mm objective; z-stacks of the biofilms were obtained using the blue and green lasers, for the whole biofilm thickness. .. Z-stacks were then analyzed using Volocity software to acquire the volume occupied by the cells in the green channel (overexpression mutant, expressing GFP) and by the cells in the blue channel (control strain, expressing BFP).

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  • 88
    Carl Zeiss axio imager z2 upright microscope
    Effect of prkC disruption on chaining morphotype during different phases of bacterial growth. (A) Growth kinetics of BAS WT. BAS WT strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (B) Growth kinetics of BAS Δ prkC . BAS Δ prkC strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (C) Phase contrast images of BAS WT and BAS Δ prkC strains at different phases of bacterial growth cycle. Cells were grown at 37°C in LB broth and 1 ml sample was harvested at time points indicated in Fig. 2A and Fig. 2B . Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss <t>Axio</t> Imager Z2 Upright Microscope. Scale bar represents 10 μm.
    Axio Imager Z2 Upright Microscope, supplied by Carl Zeiss, used in various techniques. Bioz Stars score: 88/100, based on 24 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    92
    Carl Zeiss axioimager z2 epifluorescence upright microscope
    Scarv1 cells expressing ScArv1 C27A accumulates cytosolic ER membrane structures. S . cerevisiae cells were grown in the appropriate plasmid selection medium. Cells were transformed with YCplac111-RTN2-GFP (RTN2 under its own promoter in CEN/ARS LEU2 vector). For microscopy studies, cells were diluted to approximately OD 600nm 0.15. Cells were imaged using a Zeiss <t>AxioImager.Z2</t> epifluorescence upright microscope with a 100X Plan-Apochromatic 1.4 numerical aperture objective lens. An increase in ER membrane fluorescence at medial (B) or cortical optical sections (D) were manually detected as described in Materials and Methods. (E) Percentage of cells displaying cytosolic ER membranes. (F) Percentage of cells displaying peripheral ER aggregates. 300–500 cells were counted in 3 individual experiments. Arrows in panels B D point out cytosolic ER membranes and peripheral ER aggregates, respectively. White bar represents 10 um. * p ≤ 0 . 01 ; ** p ≤ 0 . 001 ; *** p ≤ 0 . 0001 .
    Axioimager Z2 Epifluorescence Upright Microscope, supplied by Carl Zeiss, used in various techniques. Bioz Stars score: 92/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Effect of prkC disruption on chaining morphotype during different phases of bacterial growth. (A) Growth kinetics of BAS WT. BAS WT strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (B) Growth kinetics of BAS Δ prkC . BAS Δ prkC strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (C) Phase contrast images of BAS WT and BAS Δ prkC strains at different phases of bacterial growth cycle. Cells were grown at 37°C in LB broth and 1 ml sample was harvested at time points indicated in Fig. 2A and Fig. 2B . Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm.

    Journal: bioRxiv

    Article Title: Bacillus anthracis chain length, a virulence determinant, is regulated by a transmembrane Ser/Thr protein kinase PrkC

    doi: 10.1101/2020.03.15.992834

    Figure Lengend Snippet: Effect of prkC disruption on chaining morphotype during different phases of bacterial growth. (A) Growth kinetics of BAS WT. BAS WT strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (B) Growth kinetics of BAS Δ prkC . BAS Δ prkC strain was grown in LB broth at 37°C. Absorbance [OD ( A600 nm )] was recorded at the indicated time points. Error bars denote standard deviation, n = 3. (C) Phase contrast images of BAS WT and BAS Δ prkC strains at different phases of bacterial growth cycle. Cells were grown at 37°C in LB broth and 1 ml sample was harvested at time points indicated in Fig. 2A and Fig. 2B . Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm.

    Article Snippet: The cells were then observed under a 100 x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope.

    Techniques: Standard Deviation, Microscopy

    prkC disruption results in bacteria with short chain length. (A) Photograph of culture sediments in microcentrifuge tubes after standing incubation (9 hr) at room temperature of BAS WT (left) and BAS Δ prkC (right) grown in LB media. (B) Phase contrast images of BAS WT, BAS Δ prkC and BAS Δ prkC :: prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and 1 ml sample was taken from cultures in mid-log phase. Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm. (C) Scanning electron microscopy of BAS WT and BAS Δ prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and harvested in mid-log phase. These were then washed with 0.1 M sodium phosphate buffer and fixed with Karnovasky’s fixative followed by 1% osmium tetroxide. A critical point drying technique was used for drying the samples followed by gold coating of 10 nm using an aluminium stubs coated with agar sputter. Cells were visualized under Zeiss Evo LS15. Scale bar represent 2 μm, magnification-5000X.

    Journal: bioRxiv

    Article Title: Bacillus anthracis chain length, a virulence determinant, is regulated by a transmembrane Ser/Thr protein kinase PrkC

    doi: 10.1101/2020.03.15.992834

    Figure Lengend Snippet: prkC disruption results in bacteria with short chain length. (A) Photograph of culture sediments in microcentrifuge tubes after standing incubation (9 hr) at room temperature of BAS WT (left) and BAS Δ prkC (right) grown in LB media. (B) Phase contrast images of BAS WT, BAS Δ prkC and BAS Δ prkC :: prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and 1 ml sample was taken from cultures in mid-log phase. Cells were pelleted and washed with PBS and visualised under 100x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope. Scale bar represents 10 μm. (C) Scanning electron microscopy of BAS WT and BAS Δ prkC strains in mid-log phase. Cells were grown in LB broth at 37°C and harvested in mid-log phase. These were then washed with 0.1 M sodium phosphate buffer and fixed with Karnovasky’s fixative followed by 1% osmium tetroxide. A critical point drying technique was used for drying the samples followed by gold coating of 10 nm using an aluminium stubs coated with agar sputter. Cells were visualized under Zeiss Evo LS15. Scale bar represent 2 μm, magnification-5000X.

    Article Snippet: The cells were then observed under a 100 x/1.4 oil DIC objective of Zeiss Axio Imager Z2 Upright Microscope.

    Techniques: Incubation, Microscopy, Electron Microscopy

    Scarv1 cells expressing ScArv1 C27A accumulates cytosolic ER membrane structures. S . cerevisiae cells were grown in the appropriate plasmid selection medium. Cells were transformed with YCplac111-RTN2-GFP (RTN2 under its own promoter in CEN/ARS LEU2 vector). For microscopy studies, cells were diluted to approximately OD 600nm 0.15. Cells were imaged using a Zeiss AxioImager.Z2 epifluorescence upright microscope with a 100X Plan-Apochromatic 1.4 numerical aperture objective lens. An increase in ER membrane fluorescence at medial (B) or cortical optical sections (D) were manually detected as described in Materials and Methods. (E) Percentage of cells displaying cytosolic ER membranes. (F) Percentage of cells displaying peripheral ER aggregates. 300–500 cells were counted in 3 individual experiments. Arrows in panels B D point out cytosolic ER membranes and peripheral ER aggregates, respectively. White bar represents 10 um. * p ≤ 0 . 01 ; ** p ≤ 0 . 001 ; *** p ≤ 0 . 0001 .

    Journal: PLoS ONE

    Article Title: An Erg11 lanosterol 14-α-demethylase-Arv1 complex is required for Candida albicans virulence

    doi: 10.1371/journal.pone.0235746

    Figure Lengend Snippet: Scarv1 cells expressing ScArv1 C27A accumulates cytosolic ER membrane structures. S . cerevisiae cells were grown in the appropriate plasmid selection medium. Cells were transformed with YCplac111-RTN2-GFP (RTN2 under its own promoter in CEN/ARS LEU2 vector). For microscopy studies, cells were diluted to approximately OD 600nm 0.15. Cells were imaged using a Zeiss AxioImager.Z2 epifluorescence upright microscope with a 100X Plan-Apochromatic 1.4 numerical aperture objective lens. An increase in ER membrane fluorescence at medial (B) or cortical optical sections (D) were manually detected as described in Materials and Methods. (E) Percentage of cells displaying cytosolic ER membranes. (F) Percentage of cells displaying peripheral ER aggregates. 300–500 cells were counted in 3 individual experiments. Arrows in panels B D point out cytosolic ER membranes and peripheral ER aggregates, respectively. White bar represents 10 um. * p ≤ 0 . 01 ; ** p ≤ 0 . 001 ; *** p ≤ 0 . 0001 .

    Article Snippet: Cells were imaged live at room temperature using a Zeiss AxioImager.Z2 epifluorescence upright microscope with a 100X Plan-Apochromatic 1.4 numerical aperture (NA) objective lens (Carl Zeiss Ltd, Jena, Germany).

    Techniques: Expressing, Plasmid Preparation, Selection, Transformation Assay, Microscopy, Fluorescence