corti  (Qiagen)


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    QIAshredder
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    For simple and rapid homogenization of cell and tissue lysates Kit contents Qiagen QIAshredder 50 Disposable Cell lysate Homogenizers for use in Nucleic acid preps Caps For Simple and Rapid Homogenization of Cell and Tissue Lysates Replaces Syringe and needle Homogenization Reduces Loss of Sample Material Eliminates Cross contamination Between Samples Filters out Insoluble Debris and Reduces Viscosity Spin column Format QIAshredder Homogenizer Placed in a Collection Tube and Centrifuged Benefits Replaces syringe and needle homogenization Reduces loss of sample material Eliminates cross contamination between samples Filters out insoluble debris and reduces viscosity
    Catalog Number:
    79654
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    QIAshredder
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    Structured Review

    Qiagen corti
    QIAshredder
    For simple and rapid homogenization of cell and tissue lysates Kit contents Qiagen QIAshredder 50 Disposable Cell lysate Homogenizers for use in Nucleic acid preps Caps For Simple and Rapid Homogenization of Cell and Tissue Lysates Replaces Syringe and needle Homogenization Reduces Loss of Sample Material Eliminates Cross contamination Between Samples Filters out Insoluble Debris and Reduces Viscosity Spin column Format QIAshredder Homogenizer Placed in a Collection Tube and Centrifuged Benefits Replaces syringe and needle homogenization Reduces loss of sample material Eliminates cross contamination between samples Filters out insoluble debris and reduces viscosity
    https://www.bioz.com/result/corti/product/Qiagen
    Average 92 stars, based on 57828 article reviews
    Price from $9.99 to $1999.99
    corti - by Bioz Stars, 2020-04
    92/100 stars

    Images

    1) Product Images from "An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice"

    Article Title: An ENU-induced mutation of miR-96 associated with progressive hearing loss in mice

    Journal: Nature genetics

    doi: 10.1038/ng.369

    Ocm , Slc26a5 , Pitpnm1 , Ptpr1 and Gfi1 expression in diminuendo a , Quantitative real-time PCR on cDNA generated from normalised RNA from the organs of Corti of 4 day old littermates. Ocm , Slc26a5 , Ptprq and Gfi1 are downregulated in heterozygotes and homozygotes. Error bars represent standard deviation. Quantities normalised to Hprt1 levels; Ngfr is expressed in support cells adjacent to hair cells 30 and was used to assess the quantity of sensory material. Ngfr : Wildtype, n=12, mean=1.01±0.12 (s.d.); heterozygote, n=12, mean=0.89±0.35 (s.d.); homozygote, n=12, mean=0.99±0.17 (s.d.) Ocm : Wildtype, n=9, mean=1.01±0.15 (s.d.); heterozygote, n=9, mean=0.07±0.04 (s.d.); homozygote, n=9, mean=0.003±0.001 (s.d.) Slc26a5 : Wildtype, n=9, mean=1.01±0.14 (s.d.); heterozygote, n=9, mean=0.22±0.11 (s.d.); homozygote, n=9, mean=0.02±0.01 (s.d.) Gfi1 : Wildtype, n=9, mean=1.01±0.12 (s.d.); heterozygote, n=9, mean=0.88±0.12 (s.d.); homozygote, n=9, mean=0.66±0.14 (s.d.) Ptprq : Wildtype, n=9, mean=1.01±0.15 (s.d.); heterozygote, n=9, mean=0.62±0.18 (s.d.); homozygote, n=9, mean=0.56±0.20 (s.d.) Pitpnm1 : Wildtype n=8, mean=1.00±0.09 (s.d.); heterozygote, n=9, mean=0.80±0.29 (s.d.); homozygote, n=9, mean=0.78±0.27 (s.d.). Three animals were used for each genotype and DNA from each was run in triplicate. T-tests: Ngfr heterozygote p=0.25 (Welch's t-test), homozygote p=0.75 (Student's t-test); Ocm heterozygote p=1.51×10 −8 (Welch's t-test), homozygote p=3.46×10 −8 (Welch's t-test); Slc26a5 heterozygote p=7.73×10 −10 (Student's t-test), homozygote p=3.37×10 −8 (Welch's t-test); Gfi1 heterozygote p=0.038 (Student's t-test), homozygote p=3.39×10 −5 (Student's t-test); Ptprq heterozygote p=1.37×10 −4 (Student's t-test), homozygote p=6.46×10 −5 (Student's t-test); Pitpnm1 heterozygote p=0.084 (Welch's t-test), homozygote p=0.35 (Student's t-test); α=0.05. b-k , location of oncomodulin ( b, c ), prestin ( d, h ), Pitpnm1 ( e , i ), Ptprq ( f , j ) and Gfi1 ( g , k ) in 5-day old wildtype ( b, d-g ) and homozygote ( c, h-k ) littermates. Scale bars = 10μm.
    Figure Legend Snippet: Ocm , Slc26a5 , Pitpnm1 , Ptpr1 and Gfi1 expression in diminuendo a , Quantitative real-time PCR on cDNA generated from normalised RNA from the organs of Corti of 4 day old littermates. Ocm , Slc26a5 , Ptprq and Gfi1 are downregulated in heterozygotes and homozygotes. Error bars represent standard deviation. Quantities normalised to Hprt1 levels; Ngfr is expressed in support cells adjacent to hair cells 30 and was used to assess the quantity of sensory material. Ngfr : Wildtype, n=12, mean=1.01±0.12 (s.d.); heterozygote, n=12, mean=0.89±0.35 (s.d.); homozygote, n=12, mean=0.99±0.17 (s.d.) Ocm : Wildtype, n=9, mean=1.01±0.15 (s.d.); heterozygote, n=9, mean=0.07±0.04 (s.d.); homozygote, n=9, mean=0.003±0.001 (s.d.) Slc26a5 : Wildtype, n=9, mean=1.01±0.14 (s.d.); heterozygote, n=9, mean=0.22±0.11 (s.d.); homozygote, n=9, mean=0.02±0.01 (s.d.) Gfi1 : Wildtype, n=9, mean=1.01±0.12 (s.d.); heterozygote, n=9, mean=0.88±0.12 (s.d.); homozygote, n=9, mean=0.66±0.14 (s.d.) Ptprq : Wildtype, n=9, mean=1.01±0.15 (s.d.); heterozygote, n=9, mean=0.62±0.18 (s.d.); homozygote, n=9, mean=0.56±0.20 (s.d.) Pitpnm1 : Wildtype n=8, mean=1.00±0.09 (s.d.); heterozygote, n=9, mean=0.80±0.29 (s.d.); homozygote, n=9, mean=0.78±0.27 (s.d.). Three animals were used for each genotype and DNA from each was run in triplicate. T-tests: Ngfr heterozygote p=0.25 (Welch's t-test), homozygote p=0.75 (Student's t-test); Ocm heterozygote p=1.51×10 −8 (Welch's t-test), homozygote p=3.46×10 −8 (Welch's t-test); Slc26a5 heterozygote p=7.73×10 −10 (Student's t-test), homozygote p=3.37×10 −8 (Welch's t-test); Gfi1 heterozygote p=0.038 (Student's t-test), homozygote p=3.39×10 −5 (Student's t-test); Ptprq heterozygote p=1.37×10 −4 (Student's t-test), homozygote p=6.46×10 −5 (Student's t-test); Pitpnm1 heterozygote p=0.084 (Welch's t-test), homozygote p=0.35 (Student's t-test); α=0.05. b-k , location of oncomodulin ( b, c ), prestin ( d, h ), Pitpnm1 ( e , i ), Ptprq ( f , j ) and Gfi1 ( g , k ) in 5-day old wildtype ( b, d-g ) and homozygote ( c, h-k ) littermates. Scale bars = 10μm.

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Generated, Standard Deviation

    2) Product Images from "Exploring regulatory networks of miR-96 in the developing inner ear"

    Article Title: Exploring regulatory networks of miR-96 in the developing inner ear

    Journal: Scientific Reports

    doi: 10.1038/srep23363

    Testing predicted targets of miR-96 and important nodes from the regulatory network. qRTPCR was carried out on cDNA from P4 organs of Corti in wildtype (green) and diminuendo homozygote (red) littermates to test gene expression changes. Error bars are standard deviation (*adjusted P
    Figure Legend Snippet: Testing predicted targets of miR-96 and important nodes from the regulatory network. qRTPCR was carried out on cDNA from P4 organs of Corti in wildtype (green) and diminuendo homozygote (red) littermates to test gene expression changes. Error bars are standard deviation (*adjusted P

    Techniques Used: Expressing, Standard Deviation

    Testing gene expression in diminuendo homozygotes. qRTPCR was carried out on cDNA from P4 organs of Corti in wildtype (green) and diminuendo homozygote (red) littermates to test gene expression changes. Error bars are standard deviation (*adjusted P
    Figure Legend Snippet: Testing gene expression in diminuendo homozygotes. qRTPCR was carried out on cDNA from P4 organs of Corti in wildtype (green) and diminuendo homozygote (red) littermates to test gene expression changes. Error bars are standard deviation (*adjusted P

    Techniques Used: Expressing, Standard Deviation

    3) Product Images from "Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line"

    Article Title: Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line

    Journal: Biomedical Journal

    doi: 10.1016/j.bj.2018.05.002

    The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.
    Figure Legend Snippet: The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.

    Techniques Used: Expressing, Activation Assay

    Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.
    Figure Legend Snippet: Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.

    Techniques Used: Expressing, Polymerase Chain Reaction

    Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).
    Figure Legend Snippet: Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).

    Techniques Used: Irradiation

    4) Product Images from "Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium 'Candidatus Liberibacter asiaticus' by Direct PCR from the Midrib Extract"

    Article Title: Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium 'Candidatus Liberibacter asiaticus' by Direct PCR from the Midrib Extract

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0057011

    View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.
    Figure Legend Snippet: View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.

    Techniques Used: Derivative Assay, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Infection

    5) Product Images from "Simvastatin induces cell cycle arrest and inhibits proliferation of bladder cancer cells via PPARγ signalling pathway"

    Article Title: Simvastatin induces cell cycle arrest and inhibits proliferation of bladder cancer cells via PPARγ signalling pathway

    Journal: Scientific Reports

    doi: 10.1038/srep35783

    Transcriptome profiling of bladder cancer compared to normal bladder tissues pointed out the PPAR family. ( a ) Heat map of the differentially expressed genes in three bladder cancer tissues compared with three normal bladder tissues. Red color indicated upregulated genes and green color indicated downregulated genes. ( b ) GO-map network analysis by GCBI platform revealed fatty acid biosynthesis and glycerolipid metabolism were linked with bladder cancer via PPAR and ErbB signalling pathways, as well as a close correlation between bladder cancer and cell cycle. ( c ) Semiquantitative RT-PCR analysis for alterations of PPAR family ( PPARα , PPARβ and PPAR γ) using pooled total RNA isolated from the three bladder cancer tissues versus three normal bladder tissues. The expression of the GAPDH mRNA was used as a loading control. ( d ) ELISA analysis revealed the relative PPARγ DNA-binding activity in the BCa tissues was significantly decreased comparing with the normal bladder tissues (n = 3). *p
    Figure Legend Snippet: Transcriptome profiling of bladder cancer compared to normal bladder tissues pointed out the PPAR family. ( a ) Heat map of the differentially expressed genes in three bladder cancer tissues compared with three normal bladder tissues. Red color indicated upregulated genes and green color indicated downregulated genes. ( b ) GO-map network analysis by GCBI platform revealed fatty acid biosynthesis and glycerolipid metabolism were linked with bladder cancer via PPAR and ErbB signalling pathways, as well as a close correlation between bladder cancer and cell cycle. ( c ) Semiquantitative RT-PCR analysis for alterations of PPAR family ( PPARα , PPARβ and PPAR γ) using pooled total RNA isolated from the three bladder cancer tissues versus three normal bladder tissues. The expression of the GAPDH mRNA was used as a loading control. ( d ) ELISA analysis revealed the relative PPARγ DNA-binding activity in the BCa tissues was significantly decreased comparing with the normal bladder tissues (n = 3). *p

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Isolation, Expressing, Enzyme-linked Immunosorbent Assay, Binding Assay, Activity Assay, BIA-KA

    6) Product Images from "Adenovirus Type 5 Rupture of Lysosomes Leads to Cathepsin B-Dependent Mitochondrial Stress and Production of Reactive Oxygen Species ▿"

    Article Title: Adenovirus Type 5 Rupture of Lysosomes Leads to Cathepsin B-Dependent Mitochondrial Stress and Production of Reactive Oxygen Species ▿

    Journal: Journal of Virology

    doi: 10.1128/JVI.00675-11

    Cathepsin B and cytochrome c release during Ad5 infection and Ad5-induced ROS in the presence of the cathepsin B inhibitor Ca074me. (A) Two million PMA-differentiated THP-1 cells were left untreated, infected with Ad5 at 100,000 ppc, or infected with ts 1 mutant adenovirus at 100,000 ppc for 30 min. Cell membranes were selectively lysed with cytosolic extraction buffer containing 50 μg/ml digitonin. Cell lysates were run on SDS-PAGE and transferred to a nitrocellulose membrane. Western blotting detected cytoplasmic cathepsin B (catB) and cytochrome c (cytC). (B) PMA-differentiated THP-1 cells were serum starved for 3 h and then incubated with 10 μM DCFDA for 30 min, washed, pretreated with the cathepsin inhibitor Ca074me (100 μM) or DMF control for 1 h, and then left untreated (white bars) or incubated with Ad5 at 250,000 ppc (black bars). DCF fluorescence was measured on a fluorescent plate reader. The graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. Significance was determined by Student's t test (unpaired), where * indicates P
    Figure Legend Snippet: Cathepsin B and cytochrome c release during Ad5 infection and Ad5-induced ROS in the presence of the cathepsin B inhibitor Ca074me. (A) Two million PMA-differentiated THP-1 cells were left untreated, infected with Ad5 at 100,000 ppc, or infected with ts 1 mutant adenovirus at 100,000 ppc for 30 min. Cell membranes were selectively lysed with cytosolic extraction buffer containing 50 μg/ml digitonin. Cell lysates were run on SDS-PAGE and transferred to a nitrocellulose membrane. Western blotting detected cytoplasmic cathepsin B (catB) and cytochrome c (cytC). (B) PMA-differentiated THP-1 cells were serum starved for 3 h and then incubated with 10 μM DCFDA for 30 min, washed, pretreated with the cathepsin inhibitor Ca074me (100 μM) or DMF control for 1 h, and then left untreated (white bars) or incubated with Ad5 at 250,000 ppc (black bars). DCF fluorescence was measured on a fluorescent plate reader. The graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. Significance was determined by Student's t test (unpaired), where * indicates P

    Techniques Used: Infection, Mutagenesis, SDS Page, Western Blot, Incubation, Fluorescence

    Mitochondrial membrane destabilization upon Ad5 infection in the presence or absence of the cathepsin B inhibitor Ca074me. PMA-differentiated THP-1 cells were serum starved for 3 h and pretreated with 100 μM Ca074me for 20 min or left untreated. Cells were then incubated with CCCP, infected with Ad5, or infected with the ts 1 mutant adenovirus for 30 min, washed, and incubated with JC-1 for 15 min. Following two washes, cells were visualized by fluorescence microscopy and counted. Significance was determined by Student's t test (unpaired), where * indicates P
    Figure Legend Snippet: Mitochondrial membrane destabilization upon Ad5 infection in the presence or absence of the cathepsin B inhibitor Ca074me. PMA-differentiated THP-1 cells were serum starved for 3 h and pretreated with 100 μM Ca074me for 20 min or left untreated. Cells were then incubated with CCCP, infected with Ad5, or infected with the ts 1 mutant adenovirus for 30 min, washed, and incubated with JC-1 for 15 min. Following two washes, cells were visualized by fluorescence microscopy and counted. Significance was determined by Student's t test (unpaired), where * indicates P

    Techniques Used: Infection, Incubation, Mutagenesis, Fluorescence, Microscopy

    ROS production in response to Ad5 infection in the presence or absence of TLR9 knockdown. (A) PMA-differentiated THP-1 control cells (black bars) and THP-1-TLR9KD cells (white bars) were serum starved for 3 h and either left untreated (NT) or infected with Ad5 at 30,000 ppc for 6 h. Secreted IL-1β was measured by ELISA. (B) PMA-differentiated THP-1 and TLR9 knockdown (KD) cells were serum starved for 3 h then incubated with 10 μM DCFDA for 30 min, washed, and then left untreated (open squares, THP-1 cells; closed squares, TLR9KD cells) or infected with Ad5 at 500,000 ppc (open triangles, THP-1 cells; closed triangles, TLR9KD cells). The graph depicts relative DCF fluorescence intensity (RFI) over time. (Inset) Western blot for TLR9 demonstrating efficient knockdown. Significance was determined by Student's t test (unpaired) where * indicates P
    Figure Legend Snippet: ROS production in response to Ad5 infection in the presence or absence of TLR9 knockdown. (A) PMA-differentiated THP-1 control cells (black bars) and THP-1-TLR9KD cells (white bars) were serum starved for 3 h and either left untreated (NT) or infected with Ad5 at 30,000 ppc for 6 h. Secreted IL-1β was measured by ELISA. (B) PMA-differentiated THP-1 and TLR9 knockdown (KD) cells were serum starved for 3 h then incubated with 10 μM DCFDA for 30 min, washed, and then left untreated (open squares, THP-1 cells; closed squares, TLR9KD cells) or infected with Ad5 at 500,000 ppc (open triangles, THP-1 cells; closed triangles, TLR9KD cells). The graph depicts relative DCF fluorescence intensity (RFI) over time. (Inset) Western blot for TLR9 demonstrating efficient knockdown. Significance was determined by Student's t test (unpaired) where * indicates P

    Techniques Used: Infection, Enzyme-linked Immunosorbent Assay, Incubation, Fluorescence, Western Blot

    Ad5-induced ROS production and the role of ROS in Ad5-induced TNF-α secretion. (A) PMA-differentiated THP-1 cells were serum starved for 3 h and either left untreated (black bars) or pretreated for 10 min with 30 mM N -acetyl-cysteine (gray bars) or with 10 μM rotenone (white bars), and then cells were left uninfected (NT) or infected with Ad5 at 30,000 ppc in the continued presence of drug for 4 h. Secreted TNF-α was measured by ELISA. (B) PMA-differentiated THP-1 cells were serum starved for 3 h and then incubated with 10 μM DCFDA for 30 min, washed, and left untreated (open squares), infected with ts 1 mutant adenovirus (Ad2 ts 1) at 500,000 ppc (open circles), or infected with Ad5 at 50,000 ppc (closed squares), 100,000 ppc (closed circles), or 500,000 ppc (closed triangles). DCF fluorescence was measured on a fluorescent plate reader at an excitation wavelength of 485 nm and emission wavelength of 520 nm. The graph depicts DCF relative fluorescence intensity (normalized to time zero) over time.
    Figure Legend Snippet: Ad5-induced ROS production and the role of ROS in Ad5-induced TNF-α secretion. (A) PMA-differentiated THP-1 cells were serum starved for 3 h and either left untreated (black bars) or pretreated for 10 min with 30 mM N -acetyl-cysteine (gray bars) or with 10 μM rotenone (white bars), and then cells were left uninfected (NT) or infected with Ad5 at 30,000 ppc in the continued presence of drug for 4 h. Secreted TNF-α was measured by ELISA. (B) PMA-differentiated THP-1 cells were serum starved for 3 h and then incubated with 10 μM DCFDA for 30 min, washed, and left untreated (open squares), infected with ts 1 mutant adenovirus (Ad2 ts 1) at 500,000 ppc (open circles), or infected with Ad5 at 50,000 ppc (closed squares), 100,000 ppc (closed circles), or 500,000 ppc (closed triangles). DCF fluorescence was measured on a fluorescent plate reader at an excitation wavelength of 485 nm and emission wavelength of 520 nm. The graph depicts DCF relative fluorescence intensity (normalized to time zero) over time.

    Techniques Used: Infection, Enzyme-linked Immunosorbent Assay, Incubation, Mutagenesis, Fluorescence

    ROS production in response to Ad5 in the presence or absence of gp91phox (Nox2) knockdown. (A) RNA was isolated from THP-1 control cells and THP-1-gp91phox knockdown cells, and subjected to qRT-PCR using primer sets for gp91phox and β-actin. Relative gp91phox expression was generated using the 2 −ΔΔ CT method where the fold change in gp91phox expression was normalized to the housekeeping gene β-actin and gp91phox expression in the THP-1 control cells is set to 1. (B) PMA-differentiated THP-1 control cells (white bars) and THP-1-gp91phox knockdown cells (black bars) were serum starved for 3 h then incubated with 10 μM DCFDA for 30 min, washed, and left untreated, treated with Ad5 at 100,000 ppc, or treated with 5 mM ATP. DCF fluorescence was measured on a fluorescent plate reader. Graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. Significance was determined by Student's t test (unpaired), where * indicates P
    Figure Legend Snippet: ROS production in response to Ad5 in the presence or absence of gp91phox (Nox2) knockdown. (A) RNA was isolated from THP-1 control cells and THP-1-gp91phox knockdown cells, and subjected to qRT-PCR using primer sets for gp91phox and β-actin. Relative gp91phox expression was generated using the 2 −ΔΔ CT method where the fold change in gp91phox expression was normalized to the housekeeping gene β-actin and gp91phox expression in the THP-1 control cells is set to 1. (B) PMA-differentiated THP-1 control cells (white bars) and THP-1-gp91phox knockdown cells (black bars) were serum starved for 3 h then incubated with 10 μM DCFDA for 30 min, washed, and left untreated, treated with Ad5 at 100,000 ppc, or treated with 5 mM ATP. DCF fluorescence was measured on a fluorescent plate reader. Graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. Significance was determined by Student's t test (unpaired), where * indicates P

    Techniques Used: Isolation, Quantitative RT-PCR, Expressing, Generated, Incubation, Fluorescence

    Ad5-induced ROS production and IL-1β release in the presence or absence of Bcl-2 overexpression. (A) PMA-differentiated THP-1 control cells and THP-1-Bcl-2 cells were serum starved for 3 h and then incubated with 10 μM DCFDA for 30 min, washed, and left untreated (white bars) or infected with Ad5 at 500,000 ppc (black bars). DCF fluorescence was measured on a fluorescent plate reader. Graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. (B) PMA-differentiated THP-1 control cells (black bars) and THP-1-Bcl-2 cells (white bars) were serum starved for 3 h, pretreated with the TLR2 ligand PAM3CSK4, and infected with Ad5 at 50,000 ppc for 2 h. Secreted IL-1β was measured by ELISA. (Inset) Western blot demonstrating Bcl-2 protein levels. ctl, control. Significance was determined by Student's t test (unpaired), where * indicates P
    Figure Legend Snippet: Ad5-induced ROS production and IL-1β release in the presence or absence of Bcl-2 overexpression. (A) PMA-differentiated THP-1 control cells and THP-1-Bcl-2 cells were serum starved for 3 h and then incubated with 10 μM DCFDA for 30 min, washed, and left untreated (white bars) or infected with Ad5 at 500,000 ppc (black bars). DCF fluorescence was measured on a fluorescent plate reader. Graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. (B) PMA-differentiated THP-1 control cells (black bars) and THP-1-Bcl-2 cells (white bars) were serum starved for 3 h, pretreated with the TLR2 ligand PAM3CSK4, and infected with Ad5 at 50,000 ppc for 2 h. Secreted IL-1β was measured by ELISA. (Inset) Western blot demonstrating Bcl-2 protein levels. ctl, control. Significance was determined by Student's t test (unpaired), where * indicates P

    Techniques Used: Over Expression, Incubation, Infection, Fluorescence, Enzyme-linked Immunosorbent Assay, Western Blot, CTL Assay

    7) Product Images from "Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer"

    Article Title: Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer

    Journal: Oncotarget

    doi: 10.18632/oncotarget.24764

    Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p
    Figure Legend Snippet: Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p

    Techniques Used: Expressing, Software, Western Blot, Real-time Polymerase Chain Reaction

    8) Product Images from "Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer"

    Article Title: Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer

    Journal: Oncotarget

    doi: 10.18632/oncotarget.24764

    Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p
    Figure Legend Snippet: Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p

    Techniques Used: Expressing, Software, Western Blot, Real-time Polymerase Chain Reaction

    9) Product Images from "New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures"

    Article Title: New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-8-188

    Study concept . (A) Total RNA of each of the first 24 samples had been extracted following three different total RNA purification methods A, B, and C. Method A: lysis of the mononuclear cells, followed by lysate homogenization (to reduce viscosity caused by high-molecular-weight cellular components and cell debris) using a biopolymer shredding system in a microcentrifuge spin-column format (QIAshredder, Qiagen) followed by total RNA purification (RNeasy Mini Kit, Qiagen). Method B: TRIzol RNA isolation (Invitrogen). Method C: TRIzol RNA isolation (Invitrogen) followed by an RNeasy purification step (RNeasy Mini Kit, Qiagen). The RNA purification step combines the selective binding properties of a silica-based membrane with the speed of microspin technology. It allows only RNA longer than 200 bases to bind to the silica membrane, providing an enriching for mRNA since nucleotides shorter than 200 nucleotides are selectively excluded. (B) For each of three additional samples, nine aliquots of mononuclear cells had been collected. Total RNA has been processed for each aliquot following one of the three methods and for each method three independent technical replicates were performed (A,A,A, B,B,B, C,C,C).
    Figure Legend Snippet: Study concept . (A) Total RNA of each of the first 24 samples had been extracted following three different total RNA purification methods A, B, and C. Method A: lysis of the mononuclear cells, followed by lysate homogenization (to reduce viscosity caused by high-molecular-weight cellular components and cell debris) using a biopolymer shredding system in a microcentrifuge spin-column format (QIAshredder, Qiagen) followed by total RNA purification (RNeasy Mini Kit, Qiagen). Method B: TRIzol RNA isolation (Invitrogen). Method C: TRIzol RNA isolation (Invitrogen) followed by an RNeasy purification step (RNeasy Mini Kit, Qiagen). The RNA purification step combines the selective binding properties of a silica-based membrane with the speed of microspin technology. It allows only RNA longer than 200 bases to bind to the silica membrane, providing an enriching for mRNA since nucleotides shorter than 200 nucleotides are selectively excluded. (B) For each of three additional samples, nine aliquots of mononuclear cells had been collected. Total RNA has been processed for each aliquot following one of the three methods and for each method three independent technical replicates were performed (A,A,A, B,B,B, C,C,C).

    Techniques Used: Purification, Lysis, Homogenization, Molecular Weight, Isolation, Binding Assay

    10) Product Images from "Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium 'Candidatus Liberibacter asiaticus' by Direct PCR from the Midrib Extract"

    Article Title: Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium 'Candidatus Liberibacter asiaticus' by Direct PCR from the Midrib Extract

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0057011

    View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.
    Figure Legend Snippet: View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.

    Techniques Used: Derivative Assay, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Infection

    11) Product Images from "Pitpnm1 is expressed in hair cells during development but is not required for hearing"

    Article Title: Pitpnm1 is expressed in hair cells during development but is not required for hearing

    Journal: Neuroscience

    doi: 10.1016/j.neuroscience.2013.06.045

    Organ of Corti RT-PCR for Pitpnm genes. RT-PCR results showing bands for Pitpnm1 (left), Pitpnm2 (centre) and Pitpnm3 (right) from cDNA from the organ of Corti of three separate mice (A–C). Ladder band size is shown on each figure; the Pitpnm bands are between 200 and 350 bp in size.
    Figure Legend Snippet: Organ of Corti RT-PCR for Pitpnm genes. RT-PCR results showing bands for Pitpnm1 (left), Pitpnm2 (centre) and Pitpnm3 (right) from cDNA from the organ of Corti of three separate mice (A–C). Ladder band size is shown on each figure; the Pitpnm bands are between 200 and 350 bp in size.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Mouse Assay

    12) Product Images from "Decreased TRPM7 inhibits activities and induces apoptosis of bladder cancer cells via ERK1/2 pathway"

    Article Title: Decreased TRPM7 inhibits activities and induces apoptosis of bladder cancer cells via ERK1/2 pathway

    Journal: Oncotarget

    doi: 10.18632/oncotarget.12146

    TRPM7 is upregulated in the BCa tissues and correlated with EMT markers ( A ) qRT-PCR analysis of relative gene expression of TRPM7 in total RNA isolated from ten BCa tissues at stage II, comparing with ten normal bladder tissues. Significance of TRPM7 expression difference was analyzed using T-test . * p
    Figure Legend Snippet: TRPM7 is upregulated in the BCa tissues and correlated with EMT markers ( A ) qRT-PCR analysis of relative gene expression of TRPM7 in total RNA isolated from ten BCa tissues at stage II, comparing with ten normal bladder tissues. Significance of TRPM7 expression difference was analyzed using T-test . * p

    Techniques Used: BIA-KA, Quantitative RT-PCR, Expressing, Isolation

    13) Product Images from "Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines"

    Article Title: Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines

    Journal: BMC Research Notes

    doi: 10.1186/s13104-017-2959-0

    Primer location and RNA isolation method affect qPCR knockdown detection. qPCR was conducted on cDNA synthesized from total RNA samples and mRNA samples. Two primer sets—one amplifying 5′ of the siRNA cut site, the other amplifying 3′ of the siRNA cut site—were compared. Relative gene expression of a snr1 , b brm , c osa and d trr was measured by qPCR in third instar larvae after ubiquitous expression of UAS - RNAi constructs with Act - Gal4 . Expression levels were normalized to the reference genes, eIF2Bγ and βCOP . Shown here, are relative expression values compared to the UAS - mCherry - RNAi control (indicated by the dotted line). Asterisks directly above bars indicate a significant knockdown compared to the control, while asterisks above brackets indicate significant differences in gene expression between different conditions—total RNA vs. mRNA, 3′ vs. 5′ primer set (*p
    Figure Legend Snippet: Primer location and RNA isolation method affect qPCR knockdown detection. qPCR was conducted on cDNA synthesized from total RNA samples and mRNA samples. Two primer sets—one amplifying 5′ of the siRNA cut site, the other amplifying 3′ of the siRNA cut site—were compared. Relative gene expression of a snr1 , b brm , c osa and d trr was measured by qPCR in third instar larvae after ubiquitous expression of UAS - RNAi constructs with Act - Gal4 . Expression levels were normalized to the reference genes, eIF2Bγ and βCOP . Shown here, are relative expression values compared to the UAS - mCherry - RNAi control (indicated by the dotted line). Asterisks directly above bars indicate a significant knockdown compared to the control, while asterisks above brackets indicate significant differences in gene expression between different conditions—total RNA vs. mRNA, 3′ vs. 5′ primer set (*p

    Techniques Used: Isolation, Real-time Polymerase Chain Reaction, Synthesized, Expressing, Construct, Activated Clotting Time Assay

    Schematic representation of the experimental setup. siRNAs direct site-specific cleavage of mRNAs, resulting in a 5′ and 3′ mRNA cleavage fragments. After RNA isolation total RNA samples consist of uncleaved mRNA transcripts and non-coding RNA, as well as undegraded 5′ and 3′ mRNA cleavage fragments. Purification of mRNA using poly-T beads excludes 5′ mRNA cleavage fragments and non-coding RNAs that are not polyadenylated. As indicated by the boxes, 5′ and 3′ primer sets could detect different species of RNA depending on the isolation method
    Figure Legend Snippet: Schematic representation of the experimental setup. siRNAs direct site-specific cleavage of mRNAs, resulting in a 5′ and 3′ mRNA cleavage fragments. After RNA isolation total RNA samples consist of uncleaved mRNA transcripts and non-coding RNA, as well as undegraded 5′ and 3′ mRNA cleavage fragments. Purification of mRNA using poly-T beads excludes 5′ mRNA cleavage fragments and non-coding RNAs that are not polyadenylated. As indicated by the boxes, 5′ and 3′ primer sets could detect different species of RNA depending on the isolation method

    Techniques Used: Isolation, Purification

    14) Product Images from "Fabricating retinal pigment epithelial cell sheets derived from human induced pluripotent stem cells in an automated closed culture system for regenerative medicine"

    Article Title: Fabricating retinal pigment epithelial cell sheets derived from human induced pluripotent stem cells in an automated closed culture system for regenerative medicine

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0212369

    TER values of hiPS-RPE cell sheets cultured by machine and manually. hiPS-RPE cell sheets were cultured manually or using the automated ACE3 system and analyzed 49 days after seeding. The TER values of the hiPS-RPE cell sheets were calculated by subtracting the value of inserts covered with collagen gels as a blank from those of the experimental inserts. Data were obtained from two independent experiments. Machine cell culture, n = 9, manual cell culture, n = 7. All data are represented as the means ± SD.
    Figure Legend Snippet: TER values of hiPS-RPE cell sheets cultured by machine and manually. hiPS-RPE cell sheets were cultured manually or using the automated ACE3 system and analyzed 49 days after seeding. The TER values of the hiPS-RPE cell sheets were calculated by subtracting the value of inserts covered with collagen gels as a blank from those of the experimental inserts. Data were obtained from two independent experiments. Machine cell culture, n = 9, manual cell culture, n = 7. All data are represented as the means ± SD.

    Techniques Used: Cell Culture

    Phase-contrast and fluorescence images of immunostaining. hiPS-RPE cell sheets were cultured for 49 days using both machine and manual culture methods. (A–E) Phase-contrast image (top of each figure) and corresponding fluorescence image (bottom of each figure) of vertical sections of machine-cultured hiPS-RPE cell sheets. (A) Immunofluorescence detection of Na/K ATPase, (B) MERTK, (C) Claudin19, (D) RPE65, and (E) PMEL17. (F–J) Phase-contrast image (top) and corresponding fluorescence image (bottom) of vertical sections of manually cultured hiPS-RPE cell sheets. (F) Immunofluorescence detection of Na, K ATPase, (G) MERTK, (H) Claudin19, (I) RPE65, and (J) PMEL17. Nuclei were stained with DAPI. Scale bars: 20 μm.
    Figure Legend Snippet: Phase-contrast and fluorescence images of immunostaining. hiPS-RPE cell sheets were cultured for 49 days using both machine and manual culture methods. (A–E) Phase-contrast image (top of each figure) and corresponding fluorescence image (bottom of each figure) of vertical sections of machine-cultured hiPS-RPE cell sheets. (A) Immunofluorescence detection of Na/K ATPase, (B) MERTK, (C) Claudin19, (D) RPE65, and (E) PMEL17. (F–J) Phase-contrast image (top) and corresponding fluorescence image (bottom) of vertical sections of manually cultured hiPS-RPE cell sheets. (F) Immunofluorescence detection of Na, K ATPase, (G) MERTK, (H) Claudin19, (I) RPE65, and (J) PMEL17. Nuclei were stained with DAPI. Scale bars: 20 μm.

    Techniques Used: Fluorescence, Immunostaining, Cell Culture, Immunofluorescence, Staining

    Real-time PCR analysis of RPE-related gene expression in hiPS-RPE cell sheets. Data were obtained from two independent experiments. Machine cell culture, n = 7, manual cell culture, n = 5. All data are represented as the means ± SD.
    Figure Legend Snippet: Real-time PCR analysis of RPE-related gene expression in hiPS-RPE cell sheets. Data were obtained from two independent experiments. Machine cell culture, n = 7, manual cell culture, n = 5. All data are represented as the means ± SD.

    Techniques Used: Real-time Polymerase Chain Reaction, Expressing, Cell Culture

    Phase-contrast and fluorescence images of immunostaining. hiPS-RPE cell sheets were cultured for 49 days using both machine and manual culture methods. (A) Schematic figure showing a cross-section of the RPE cell sheet. (B–G) Phase-contrast (B, C) and fluorescence (D–G) images of machine-cultured hiPS-RPE cell sheets. (B, D, F) Immunostaining for tight junction (ZO-1, red) and basement membrane (laminin, green) proteins. (C, E, G) Immunostaining for tight junction (ZO-1, green) and basement membrane (type IV collagen, red) proteins. (H–M) Phase-contrast (H, I) and fluorescence (J–M) images of manually cultured hiPS-RPE cell sheets. (H, J, L) Immunostaining for tight junction (ZO-1, red) and basement membrane (laminin, green) proteins. (I, K, M) Immunostaining for tight junction (ZO-1, green) and basement membrane (type IV collagen, red) proteins. Scale bars: 50 μm.
    Figure Legend Snippet: Phase-contrast and fluorescence images of immunostaining. hiPS-RPE cell sheets were cultured for 49 days using both machine and manual culture methods. (A) Schematic figure showing a cross-section of the RPE cell sheet. (B–G) Phase-contrast (B, C) and fluorescence (D–G) images of machine-cultured hiPS-RPE cell sheets. (B, D, F) Immunostaining for tight junction (ZO-1, red) and basement membrane (laminin, green) proteins. (C, E, G) Immunostaining for tight junction (ZO-1, green) and basement membrane (type IV collagen, red) proteins. (H–M) Phase-contrast (H, I) and fluorescence (J–M) images of manually cultured hiPS-RPE cell sheets. (H, J, L) Immunostaining for tight junction (ZO-1, red) and basement membrane (laminin, green) proteins. (I, K, M) Immunostaining for tight junction (ZO-1, green) and basement membrane (type IV collagen, red) proteins. Scale bars: 50 μm.

    Techniques Used: Fluorescence, Immunostaining, Cell Culture

    15) Product Images from "Altered balance between self-reactive T helper (Th)17 cells and Th10 cells and between full-length forkhead box protein 3 (FoxP3) and FoxP3 splice variants in Hashimoto's thyroiditis"

    Article Title: Altered balance between self-reactive T helper (Th)17 cells and Th10 cells and between full-length forkhead box protein 3 (FoxP3) and FoxP3 splice variants in Hashimoto's thyroiditis

    Journal: Clinical and Experimental Immunology

    doi: 10.1111/cei.12557

    T helper (Th)10 cell differentiation driven by thyroid self-antigens. Peripheral blood mononuclear cells (PBMCs) were incubated with thyroglobulin (TG), thyroid peroxidase (TPO) or Escherichia coli lipopolysaccharide for 48 h, and CD4 + Th cells were stained intracellularly for IL-10 and detected by flow cytometry. (a) Proportions of naive Th10 + cells are shown for healthy controls (HC, n = 15), patients with Graves' disease (GD, n = 11) and patients with Hashimoto's thyroiditis (HT, n = 10). (b) Corresponding proportions of memory Th10 + cells are shown. Corresponding proportions observed in the absence of antigen have been subtracted. (c) The proportion of naive Th10 + cells in GD patients ( n = 11) after TPO stimulation is shown against circulating levels of anti- thyroid stimulating hormone receptor (TSHR) antibodies (kIU/l). Spearman's rank correlation coefficient ( R s) and level of significance are shown; negative net values were included in calculations. Box-plots indicate median, interquartile range (box) and range (whiskers).
    Figure Legend Snippet: T helper (Th)10 cell differentiation driven by thyroid self-antigens. Peripheral blood mononuclear cells (PBMCs) were incubated with thyroglobulin (TG), thyroid peroxidase (TPO) or Escherichia coli lipopolysaccharide for 48 h, and CD4 + Th cells were stained intracellularly for IL-10 and detected by flow cytometry. (a) Proportions of naive Th10 + cells are shown for healthy controls (HC, n = 15), patients with Graves' disease (GD, n = 11) and patients with Hashimoto's thyroiditis (HT, n = 10). (b) Corresponding proportions of memory Th10 + cells are shown. Corresponding proportions observed in the absence of antigen have been subtracted. (c) The proportion of naive Th10 + cells in GD patients ( n = 11) after TPO stimulation is shown against circulating levels of anti- thyroid stimulating hormone receptor (TSHR) antibodies (kIU/l). Spearman's rank correlation coefficient ( R s) and level of significance are shown; negative net values were included in calculations. Box-plots indicate median, interquartile range (box) and range (whiskers).

    Techniques Used: Cell Differentiation, Incubation, Staining, Flow Cytometry, Cytometry

    Expression of total forkhead box protein 3 (FoxP3) and FoxP3Δ2 mRNA following antigenic and polyclonal stimulation. (a,b) Peripheral blood mononuclear cells (PBMCs) from healthy controls (HC; n = 8), patients with Graves' disease (GD, n = 4), and patients with Hashimoto's thyroiditis (HT, n = 4) were incubated for 18 h with anti-CD3/anti-CD28-coated beads. (c,d) Alternatively, thyroglobulin (TG), thyroid peroxidase (TPO), or Escherichia coli lipopolysaccharide (LPS) were used as stimuli. PBMCs receiving no antigenic stimulation (no antigen) served as the negative control. RNA was purified and quantitative reverse transcription–polymerase chain reaction (qRT–PCR) performed using CD4 as housekeeping gene. The expression of CD4 did not alter between the patients or healthy controls as determined by flow cytometry (data not shown). Expression of (a,c) total FoxP3 or (b,d) FoxP3Δ2, relative to the expression of CD4, was determined. Ratios of FoxP3Δ2 over total FoxP3 are shown after (e) anti-CD3/anti-CD28 stimulation or (f) antigenic stimulation. Box-plots indicate median, interquartile range (box) and range (whiskers). Brackets show differences between groups with the corresponding raw P -values (Mann–Whitney U -test). * P
    Figure Legend Snippet: Expression of total forkhead box protein 3 (FoxP3) and FoxP3Δ2 mRNA following antigenic and polyclonal stimulation. (a,b) Peripheral blood mononuclear cells (PBMCs) from healthy controls (HC; n = 8), patients with Graves' disease (GD, n = 4), and patients with Hashimoto's thyroiditis (HT, n = 4) were incubated for 18 h with anti-CD3/anti-CD28-coated beads. (c,d) Alternatively, thyroglobulin (TG), thyroid peroxidase (TPO), or Escherichia coli lipopolysaccharide (LPS) were used as stimuli. PBMCs receiving no antigenic stimulation (no antigen) served as the negative control. RNA was purified and quantitative reverse transcription–polymerase chain reaction (qRT–PCR) performed using CD4 as housekeeping gene. The expression of CD4 did not alter between the patients or healthy controls as determined by flow cytometry (data not shown). Expression of (a,c) total FoxP3 or (b,d) FoxP3Δ2, relative to the expression of CD4, was determined. Ratios of FoxP3Δ2 over total FoxP3 are shown after (e) anti-CD3/anti-CD28 stimulation or (f) antigenic stimulation. Box-plots indicate median, interquartile range (box) and range (whiskers). Brackets show differences between groups with the corresponding raw P -values (Mann–Whitney U -test). * P

    Techniques Used: Expressing, Incubation, Negative Control, Purification, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Flow Cytometry, Cytometry, MANN-WHITNEY

    T helper (Th)17 cell differentiation driven by thyroid self-antigens. Peripheral blood mononuclear cells (PBMCs) were incubated with thyroglobulin (TG), thyroid peroxidase (TPO) or Escherichia coli lipopolysaccharide (LPS) for 18 h, and CD4 + interleukin (IL)-17 + Th cells were assessed by flow cytometry. (a) Naive and memory CD4 + Th cells were identified as CD45RA + CD45R0 – events (P1) and CD45RA – CD45R0 + events (P2), respectively. (b) Th17 + cells were identified as events within the P3 gate. Left panel shows naive unstimulated CD4 + Th cells (no antigen); right panel shows naive cells stimulated with thyroglobulin (TG). The same gating strategy was applied to TPO- and LPS-stimulated cells. (c) Proportions of naive Th17 + cells in PBMC cultures derived from healthy controls (HC, n = 15), donors with Graves' disease ( n = 11) and donors with Hashimoto's thyroiditis ( n = 10). (d) Corresponding proportions of memory Th17 + cells are shown. Proportions observed in the absence of stimulating antigen have been subtracted. Box-plots indicate median, interquartile range (box) and range (whiskers). Raw P -values are shown (Mann–Whitney U -test); negative net values were included in calculations.
    Figure Legend Snippet: T helper (Th)17 cell differentiation driven by thyroid self-antigens. Peripheral blood mononuclear cells (PBMCs) were incubated with thyroglobulin (TG), thyroid peroxidase (TPO) or Escherichia coli lipopolysaccharide (LPS) for 18 h, and CD4 + interleukin (IL)-17 + Th cells were assessed by flow cytometry. (a) Naive and memory CD4 + Th cells were identified as CD45RA + CD45R0 – events (P1) and CD45RA – CD45R0 + events (P2), respectively. (b) Th17 + cells were identified as events within the P3 gate. Left panel shows naive unstimulated CD4 + Th cells (no antigen); right panel shows naive cells stimulated with thyroglobulin (TG). The same gating strategy was applied to TPO- and LPS-stimulated cells. (c) Proportions of naive Th17 + cells in PBMC cultures derived from healthy controls (HC, n = 15), donors with Graves' disease ( n = 11) and donors with Hashimoto's thyroiditis ( n = 10). (d) Corresponding proportions of memory Th17 + cells are shown. Proportions observed in the absence of stimulating antigen have been subtracted. Box-plots indicate median, interquartile range (box) and range (whiskers). Raw P -values are shown (Mann–Whitney U -test); negative net values were included in calculations.

    Techniques Used: Cell Differentiation, Incubation, Flow Cytometry, Cytometry, Derivative Assay, MANN-WHITNEY

    16) Product Images from "Altered balance between self-reactive T helper (Th)17 cells and Th10 cells and between full-length forkhead box protein 3 (FoxP3) and FoxP3 splice variants in Hashimoto's thyroiditis"

    Article Title: Altered balance between self-reactive T helper (Th)17 cells and Th10 cells and between full-length forkhead box protein 3 (FoxP3) and FoxP3 splice variants in Hashimoto's thyroiditis

    Journal: Clinical and Experimental Immunology

    doi: 10.1111/cei.12557

    Expression of total forkhead box protein 3 (FoxP3) and FoxP3Δ2 mRNA following antigenic and polyclonal stimulation. (a,b) Peripheral blood mononuclear cells (PBMCs) from healthy controls (HC; n = 8), patients with Graves' disease (GD, n = 4), and patients with Hashimoto's thyroiditis (HT, n = 4) were incubated for 18 h with anti-CD3/anti-CD28-coated beads. (c,d) Alternatively, thyroglobulin (TG), thyroid peroxidase (TPO), or Escherichia coli lipopolysaccharide (LPS) were used as stimuli. PBMCs receiving no antigenic stimulation (no antigen) served as the negative control. RNA was purified and quantitative reverse transcription–polymerase chain reaction (qRT–PCR) performed using CD4 as housekeeping gene. The expression of CD4 did not alter between the patients or healthy controls as determined by flow cytometry (data not shown). Expression of (a,c) total FoxP3 or (b,d) FoxP3Δ2, relative to the expression of CD4, was determined. Ratios of FoxP3Δ2 over total FoxP3 are shown after (e) anti-CD3/anti-CD28 stimulation or (f) antigenic stimulation. Box-plots indicate median, interquartile range (box) and range (whiskers). Brackets show differences between groups with the corresponding raw P -values (Mann–Whitney U -test). * P
    Figure Legend Snippet: Expression of total forkhead box protein 3 (FoxP3) and FoxP3Δ2 mRNA following antigenic and polyclonal stimulation. (a,b) Peripheral blood mononuclear cells (PBMCs) from healthy controls (HC; n = 8), patients with Graves' disease (GD, n = 4), and patients with Hashimoto's thyroiditis (HT, n = 4) were incubated for 18 h with anti-CD3/anti-CD28-coated beads. (c,d) Alternatively, thyroglobulin (TG), thyroid peroxidase (TPO), or Escherichia coli lipopolysaccharide (LPS) were used as stimuli. PBMCs receiving no antigenic stimulation (no antigen) served as the negative control. RNA was purified and quantitative reverse transcription–polymerase chain reaction (qRT–PCR) performed using CD4 as housekeeping gene. The expression of CD4 did not alter between the patients or healthy controls as determined by flow cytometry (data not shown). Expression of (a,c) total FoxP3 or (b,d) FoxP3Δ2, relative to the expression of CD4, was determined. Ratios of FoxP3Δ2 over total FoxP3 are shown after (e) anti-CD3/anti-CD28 stimulation or (f) antigenic stimulation. Box-plots indicate median, interquartile range (box) and range (whiskers). Brackets show differences between groups with the corresponding raw P -values (Mann–Whitney U -test). * P

    Techniques Used: Expressing, Incubation, Negative Control, Purification, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Flow Cytometry, Cytometry, MANN-WHITNEY

    17) Product Images from "Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line"

    Article Title: Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line

    Journal: Biomedical Journal

    doi: 10.1016/j.bj.2018.05.002

    The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.
    Figure Legend Snippet: The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.

    Techniques Used: Expressing, Activation Assay

    Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.
    Figure Legend Snippet: Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.

    Techniques Used: Expressing, Polymerase Chain Reaction

    Estimation of cytochrome C levels in untreated and treated MCF-7 cells. Cells treated with laser alone or MPDC alone did not lead to an increased colorometric signal when compared to the untreated cells. PDT-treated cells showed a significant increase shown as *** ( p = 0.0005) and evidence of undergoing cell damage.
    Figure Legend Snippet: Estimation of cytochrome C levels in untreated and treated MCF-7 cells. Cells treated with laser alone or MPDC alone did not lead to an increased colorometric signal when compared to the untreated cells. PDT-treated cells showed a significant increase shown as *** ( p = 0.0005) and evidence of undergoing cell damage.

    Techniques Used:

    Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).
    Figure Legend Snippet: Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).

    Techniques Used: Irradiation

    18) Product Images from "Pitpnm1 is expressed in hair cells during development but is not required for hearing"

    Article Title: Pitpnm1 is expressed in hair cells during development but is not required for hearing

    Journal: Neuroscience

    doi: 10.1016/j.neuroscience.2013.06.045

    Organ of Corti RT-PCR for Pitpnm genes. RT-PCR results showing bands for Pitpnm1 (left), Pitpnm2 (centre) and Pitpnm3 (right) from cDNA from the organ of Corti of three separate mice (A–C). Ladder band size is shown on each figure; the Pitpnm bands are between 200 and 350 bp in size.
    Figure Legend Snippet: Organ of Corti RT-PCR for Pitpnm genes. RT-PCR results showing bands for Pitpnm1 (left), Pitpnm2 (centre) and Pitpnm3 (right) from cDNA from the organ of Corti of three separate mice (A–C). Ladder band size is shown on each figure; the Pitpnm bands are between 200 and 350 bp in size.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Mouse Assay

    Expression of Pitpnm1 . Pitpnm1 expression in wildtype mice at E18.5 (A), P5 (B–E) and 9 weeks old (F–H). (A) Only inner hair cells show expression at E18.5. (B) The organ of Corti at P5, with staining in all hair cells at the apex (a) but in the inner hair cell only at the base (b). (C) and (D) are close-ups of the apical turn and basal turn respectively. (E) Fainter staining in vestibular hair cells and supporting cells of the crista at P5. (F) Staining in the inner hair cells only at 9 weeks old; (G) is a close-up of (F). (H) Staining in the macula at 9 weeks old. Positive staining is in brown; tissue is counterstained blue. Cochlear hair cells are indicated by arrowheads. (A, C–H) Scale bar = 20 μm, (B) Scale bar = 100 μm.
    Figure Legend Snippet: Expression of Pitpnm1 . Pitpnm1 expression in wildtype mice at E18.5 (A), P5 (B–E) and 9 weeks old (F–H). (A) Only inner hair cells show expression at E18.5. (B) The organ of Corti at P5, with staining in all hair cells at the apex (a) but in the inner hair cell only at the base (b). (C) and (D) are close-ups of the apical turn and basal turn respectively. (E) Fainter staining in vestibular hair cells and supporting cells of the crista at P5. (F) Staining in the inner hair cells only at 9 weeks old; (G) is a close-up of (F). (H) Staining in the macula at 9 weeks old. Positive staining is in brown; tissue is counterstained blue. Cochlear hair cells are indicated by arrowheads. (A, C–H) Scale bar = 20 μm, (B) Scale bar = 100 μm.

    Techniques Used: Expressing, Mouse Assay, Staining

    19) Product Images from "Investigation of the Role of TNF-? Converting Enzyme (TACE) in the Inhibition of Cell Surface and Soluble TNF-? Production by Acute Ethanol Exposure"

    Article Title: Investigation of the Role of TNF-? Converting Enzyme (TACE) in the Inhibition of Cell Surface and Soluble TNF-? Production by Acute Ethanol Exposure

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0029890

    Real time RT-PCR with mRNA isolated from RAW264.7 cells treated with ethanol and LPS or poly I:C. Naive groups received no treatment. A Appropriate groups were treated with ethanol for 30 min, then with LPS for further two hours. The average of two experiments, each with three replicates, were pooled. Each sample replicate was doubled in the PCR plate. 86.8 mM ethanol significantly reduced the LPS induced TNF-α mRNA expression (P
    Figure Legend Snippet: Real time RT-PCR with mRNA isolated from RAW264.7 cells treated with ethanol and LPS or poly I:C. Naive groups received no treatment. A Appropriate groups were treated with ethanol for 30 min, then with LPS for further two hours. The average of two experiments, each with three replicates, were pooled. Each sample replicate was doubled in the PCR plate. 86.8 mM ethanol significantly reduced the LPS induced TNF-α mRNA expression (P

    Techniques Used: Quantitative RT-PCR, Isolation, Polymerase Chain Reaction, Expressing

    Effect of TACE inhibition on the LPS and poly I:C induced TNF-α response in RAW264.7 cells. TNF-α levels were measured by ELISA from cell culture medium immediately after collection. Each group contained 6 samples. Naive groups received no treatment. A Cells were treated with 25 µg/ml TAPI-0, 5 µl/ml DMSO, and/or 100 ng/ml LPS. Treatments were given at the same time point and cells were incubated 2 h. B Appropriate groups were treated with 86.8 mM EtOH and incubated 30 min. Cells were treated with 25 µg/ml TAPI-0, 5 µl DMSO, and/or 50 µg/ml poly I:C, and incubated further 2 h. Bars with no shared letters are significantly different (p
    Figure Legend Snippet: Effect of TACE inhibition on the LPS and poly I:C induced TNF-α response in RAW264.7 cells. TNF-α levels were measured by ELISA from cell culture medium immediately after collection. Each group contained 6 samples. Naive groups received no treatment. A Cells were treated with 25 µg/ml TAPI-0, 5 µl/ml DMSO, and/or 100 ng/ml LPS. Treatments were given at the same time point and cells were incubated 2 h. B Appropriate groups were treated with 86.8 mM EtOH and incubated 30 min. Cells were treated with 25 µg/ml TAPI-0, 5 µl DMSO, and/or 50 µg/ml poly I:C, and incubated further 2 h. Bars with no shared letters are significantly different (p

    Techniques Used: Inhibition, Enzyme-linked Immunosorbent Assay, Cell Culture, Incubation

    Surface expression of TNF-α in RAW264.7 cells measured by flow cytometry, and TNF-α ELISA from cell culture supernatants of the same experiments. Results shown in A and B were from one experiment and results shown in C and D are from an independent experiment. Each group contained 5 samples. Cells were treated with ethanol (either 43.4 mM or 86.8 mM, as indicated in the Figure), 50 µg/ml poly I:C, 20 µg/ml TAPI-0 (with no DMSO), or a combination of these treatments. ELISA was performed from cell culture supernatants of each group. The percentage of gated cells for each group is shown in A and C . Results for TNF-α ELISA from cell culture supernatants of the cells used for flow cytometry are depicted in B and D . Values for bars designated by the same letter are not significantly different (p > 0.05); values for bars with no shared letters are significantly different (p
    Figure Legend Snippet: Surface expression of TNF-α in RAW264.7 cells measured by flow cytometry, and TNF-α ELISA from cell culture supernatants of the same experiments. Results shown in A and B were from one experiment and results shown in C and D are from an independent experiment. Each group contained 5 samples. Cells were treated with ethanol (either 43.4 mM or 86.8 mM, as indicated in the Figure), 50 µg/ml poly I:C, 20 µg/ml TAPI-0 (with no DMSO), or a combination of these treatments. ELISA was performed from cell culture supernatants of each group. The percentage of gated cells for each group is shown in A and C . Results for TNF-α ELISA from cell culture supernatants of the cells used for flow cytometry are depicted in B and D . Values for bars designated by the same letter are not significantly different (p > 0.05); values for bars with no shared letters are significantly different (p

    Techniques Used: Expressing, Flow Cytometry, Cytometry, Enzyme-linked Immunosorbent Assay, Cell Culture

    Surface expression of TNF-α on RAW264.7 cells measured by flow cytometry, and TNF-α ELISA from cell culture supernatants of the same experiments. Results shown in A and B were obtained in one experiment and results shown in C and D were obtained in an independent experiment. In some groups, no TNF-α was detected (nd). Each group contained 5 samples. Two repeat experiments are shown. Cells were treated with ethanol (either 43.4 mM or 86.8 mM), 100 ng/ml LPS or 20 µg/ml TAPI-0, or a combination of these treatments. ELISA was performed from cell culture supernatants of each group. The percentage of gated cells (positive for TNF-α surface expression by flow cytometry) for each group is shown in A C . The ELISA results from cell culture supernatants of the cells used for flow cytometry are depicted in B and D . Bars designated by the same letter are not significantly different (p > 0.05); bars with no shared letters are significantly different (p
    Figure Legend Snippet: Surface expression of TNF-α on RAW264.7 cells measured by flow cytometry, and TNF-α ELISA from cell culture supernatants of the same experiments. Results shown in A and B were obtained in one experiment and results shown in C and D were obtained in an independent experiment. In some groups, no TNF-α was detected (nd). Each group contained 5 samples. Two repeat experiments are shown. Cells were treated with ethanol (either 43.4 mM or 86.8 mM), 100 ng/ml LPS or 20 µg/ml TAPI-0, or a combination of these treatments. ELISA was performed from cell culture supernatants of each group. The percentage of gated cells (positive for TNF-α surface expression by flow cytometry) for each group is shown in A C . The ELISA results from cell culture supernatants of the cells used for flow cytometry are depicted in B and D . Bars designated by the same letter are not significantly different (p > 0.05); bars with no shared letters are significantly different (p

    Techniques Used: Expressing, Flow Cytometry, Cytometry, Enzyme-linked Immunosorbent Assay, Cell Culture

    20) Product Images from "Headbobber: A Combined Morphogenetic and Cochleosaccular Mouse Model to Study 10qter Deletions in Human Deafness"

    Article Title: Headbobber: A Combined Morphogenetic and Cochleosaccular Mouse Model to Study 10qter Deletions in Human Deafness

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0056274

    Expression analysis of Hmx3 and Hmx2 homeobox transcription factors in hb/hb and control littermates. A–B: Hmx3 expression in hb/hb mutants tested by whole mount RNA in situ hybridisation at E10.5, showing decreased expression of Hmx3 in the dorsal part of the otocyst of hb/hb mutants compared to littermate controls (arrows) C,D: RNA in situ hybridisation for Hmx3 at E12.5 in vestibular system sagittal sections. In control littermates, Hmx3 RNA is detected in the canal fusion plate (black arrowhead in C), semicircular canals (red arrowheads in C), and in the utricle and saccule (not shown) but its expression is always observed in non-sensory epithelial cells as previously reported (C). In hb/hb mutants we still detect Hmx3 mRNA in the vestibular non-sensory regions compared to the littermate controls (arrowhead in D). E,F: Hmx2 expression in vestibular system detected by in situ hybridisation on sagittal sections from hb/hb and littermate controls at E12.5. In control mice, as previously reported, Hmx2 shows a similar expression pattern to Hmx3 in the non-sensory cells and in the canal plate, in the utricle (arrow in E ) and in the canals (not shown). In hb/hb we detect Hmx2 expression only in a few cells in the non-sensory regions of the structurally abnormal vestibular system, compared to the littermate controls (arrowheads in F ). Scale bars: A,B, 0.5 mm; C–F, 100 µm. G: Quantitative real-time PCR of cDNA generated from RNA from E12.5 littermate embryo half heads. Only Hmx3, Hmx2 and Nkx1.2 mRNA levels are significantly downregulated in hb/hb compared to littermate controls. Error bars, s.d. Quantity normalised to Hprt1 levels. N = 3. *:p
    Figure Legend Snippet: Expression analysis of Hmx3 and Hmx2 homeobox transcription factors in hb/hb and control littermates. A–B: Hmx3 expression in hb/hb mutants tested by whole mount RNA in situ hybridisation at E10.5, showing decreased expression of Hmx3 in the dorsal part of the otocyst of hb/hb mutants compared to littermate controls (arrows) C,D: RNA in situ hybridisation for Hmx3 at E12.5 in vestibular system sagittal sections. In control littermates, Hmx3 RNA is detected in the canal fusion plate (black arrowhead in C), semicircular canals (red arrowheads in C), and in the utricle and saccule (not shown) but its expression is always observed in non-sensory epithelial cells as previously reported (C). In hb/hb mutants we still detect Hmx3 mRNA in the vestibular non-sensory regions compared to the littermate controls (arrowhead in D). E,F: Hmx2 expression in vestibular system detected by in situ hybridisation on sagittal sections from hb/hb and littermate controls at E12.5. In control mice, as previously reported, Hmx2 shows a similar expression pattern to Hmx3 in the non-sensory cells and in the canal plate, in the utricle (arrow in E ) and in the canals (not shown). In hb/hb we detect Hmx2 expression only in a few cells in the non-sensory regions of the structurally abnormal vestibular system, compared to the littermate controls (arrowheads in F ). Scale bars: A,B, 0.5 mm; C–F, 100 µm. G: Quantitative real-time PCR of cDNA generated from RNA from E12.5 littermate embryo half heads. Only Hmx3, Hmx2 and Nkx1.2 mRNA levels are significantly downregulated in hb/hb compared to littermate controls. Error bars, s.d. Quantity normalised to Hprt1 levels. N = 3. *:p

    Techniques Used: Expressing, In Situ, Hybridization, Mouse Assay, Real-time Polymerase Chain Reaction, Generated

    Summary of the expression patterns of selected markers of inner ear development, performed on sagittal sections from hb/hb mutants and littermate controls at different stages of development. A–D: RNA In situ hybridisation for Bmp4 E12.5 in hb/hb and littermate controls. In control mice, Bmp4 expression overlaps with the pattern detected for Hmx3 and Hmx2 , being expressed in the non-sensory cells adjacent to the organ of Corti and cristae (arrowheads in A and C). No Bmp4 expression is detected in maculae at that stage. (mu in A) In hb/hb , Bmp4 is expressed in two regions in the vestibular cyst (white arrowheads in B), which are definitely not adjacent to any sensory regions in the headbobber homozygotes at later stages. C,D : No difference in Bmp4 RNA levels has been detected in hb/hb mutant cochleae compared to their littermate controls. E–H: Sox2 immunohistochemistry in hb/hb and littermate controls at E14.5. In control mice, Sox2 is expressed in all the prosensory regions of the inner ear (arrows in E,G). In hb/hb vestibular system, Sox2 shows normal expression in the fused maculae (fm in F), which is the only vestibular prosensory patch we detect in hb/hb . Sox2 cochlear expression in hb/hb looks normal when compared with the littermate controls, suggesting a normal development of the organ of Corti at embryonic age E14.5. In addition, Sox2 marks the nuclei of both vestibular and cochlear ganglia (vg in E,F and ag in G,H), and again no differences in Sox2 expression have been detected in these cells at this stage of development. I–J : Expression of Calretinin at E14.5 of hb/hb and control littermates. At this stage Calretinin marks the developing hair cells. While the hair cells in the organ of Corti are not developing yet at this stage, a few hair cells start to develop in the maculae of normal mice (arrow in I). Calretinin expression analysis shows presence of a few normally developing hair cells in the fused maculae of hb/hb at this stage (arrow in J). K–L: p27 Kip1 expression on hb/hb and littermate controls at E14.5. P27 Kip1 at E14.5 is upregulated in cells of the sensory patch in the cochlea as they prepare to exit the cell cycle. Immunohistochemistry using P27 Kip1 antibody demonstrates that in hb/hb mutants prosensory cells this marker is expressed in the same way in the hb/hb organ of Corti, compared to littermate controls (arrows in K,L). Scale bars: 200 µm A: anterior; ag: acoustic ganglion; c: cochlea; cc: common crus; cy: vestibular cyst;D: distal; ed: endolymphatic duct; fm: fused maculae; ms: maculae sacculi; mu: maculae utriculi; oc:organ of Corti; pc: posterior semicircular canal; pcr: posterior cristae; vg: vestibular ganglion; s:saccule; sv: stria vascularis; u:utricle; s+u: utriculosaccular space; vd: vestibular diverticulum.
    Figure Legend Snippet: Summary of the expression patterns of selected markers of inner ear development, performed on sagittal sections from hb/hb mutants and littermate controls at different stages of development. A–D: RNA In situ hybridisation for Bmp4 E12.5 in hb/hb and littermate controls. In control mice, Bmp4 expression overlaps with the pattern detected for Hmx3 and Hmx2 , being expressed in the non-sensory cells adjacent to the organ of Corti and cristae (arrowheads in A and C). No Bmp4 expression is detected in maculae at that stage. (mu in A) In hb/hb , Bmp4 is expressed in two regions in the vestibular cyst (white arrowheads in B), which are definitely not adjacent to any sensory regions in the headbobber homozygotes at later stages. C,D : No difference in Bmp4 RNA levels has been detected in hb/hb mutant cochleae compared to their littermate controls. E–H: Sox2 immunohistochemistry in hb/hb and littermate controls at E14.5. In control mice, Sox2 is expressed in all the prosensory regions of the inner ear (arrows in E,G). In hb/hb vestibular system, Sox2 shows normal expression in the fused maculae (fm in F), which is the only vestibular prosensory patch we detect in hb/hb . Sox2 cochlear expression in hb/hb looks normal when compared with the littermate controls, suggesting a normal development of the organ of Corti at embryonic age E14.5. In addition, Sox2 marks the nuclei of both vestibular and cochlear ganglia (vg in E,F and ag in G,H), and again no differences in Sox2 expression have been detected in these cells at this stage of development. I–J : Expression of Calretinin at E14.5 of hb/hb and control littermates. At this stage Calretinin marks the developing hair cells. While the hair cells in the organ of Corti are not developing yet at this stage, a few hair cells start to develop in the maculae of normal mice (arrow in I). Calretinin expression analysis shows presence of a few normally developing hair cells in the fused maculae of hb/hb at this stage (arrow in J). K–L: p27 Kip1 expression on hb/hb and littermate controls at E14.5. P27 Kip1 at E14.5 is upregulated in cells of the sensory patch in the cochlea as they prepare to exit the cell cycle. Immunohistochemistry using P27 Kip1 antibody demonstrates that in hb/hb mutants prosensory cells this marker is expressed in the same way in the hb/hb organ of Corti, compared to littermate controls (arrows in K,L). Scale bars: 200 µm A: anterior; ag: acoustic ganglion; c: cochlea; cc: common crus; cy: vestibular cyst;D: distal; ed: endolymphatic duct; fm: fused maculae; ms: maculae sacculi; mu: maculae utriculi; oc:organ of Corti; pc: posterior semicircular canal; pcr: posterior cristae; vg: vestibular ganglion; s:saccule; sv: stria vascularis; u:utricle; s+u: utriculosaccular space; vd: vestibular diverticulum.

    Techniques Used: Expressing, In Situ, Hybridization, Mouse Assay, Mutagenesis, Immunohistochemistry, Marker, Mass Spectrometry, Polymerase Chain Reaction

    A–E: Trp2 expression performed on inner ear sagittal sections in hb/hb, Hmx3 KO /Hmx3 KO and control littermates at E12.5 and E16.5. A–C : Trp2 marks neural crest-derived melanoblasts at E12.5 (arrowheads in A). As shown by the arrowheads in B and C, we detect melanoblasts migrating from the neural crest to developing stria is detected in hb/hb , Hmx3 KO /Hmx3 KO , and littermate controls. D–E: While in control mice at E16.5 some intermediate cells precursors are already in the process of interdigitation in the developing stria vascularis (arrowheads in D), none are in the same process in the hb/hb mutants with only a couple of them lying outside the epithelium (arrowheads E). Moreover, Hematoxylin and Eosin counterstaining shows that the epithelium of developing stria looks immature in hb/hb compared to littermate controls (arrows in D,E). Scale bars: 10 µm. F : Cartoon of the cellular structure of stria vascularis. Adapted from [77] . G–I : Immunohistochemistry showing Laminin expression in cochlea and general cochlear morphology of hb/hb, Hmx3 KO /Hmx3 KO and control littermates at P5. Laminin is expressed in all cochlear basal lamina [63] , including stria vascularis, Reissner's membrane, root cell processes and spiral prominence (arrows in G). J–L : Laminin expression in stria vascularis of hb/hb, Hmx3 KO /Hmx3 KO and control littermates at P5. At this stage, we detect basal lamina in blood vessel endothelia (arrowhead in J) and in very small pockets below marginal cells (black arrowhead in J) in control mice. In hb/hb we detect a much stronger laminin expression (denser basal lamina) around the immature stria vascularis (arrow in K). Moreover, we observe fewer and smaller blood vessels in hb/hb compared to littermate controls (examples of blood vessels are labeled with transparent arrowheads in J,K,L). We did not detect any difference in laminin expression in Hmx3 KO /Hmx3 KO compared to littermate controls (arrowhead in L). M–O : Kcnj10 expression in the stria vascularis of hb/hb, Hmx3 KO mutants and control littermates at P5. Kcnj10 is an inward potassium channel of intermediate cells. We detect only some intermediate cells in hb/hb mutants (arrowheads in N) compared to their littermate controls at this stage (M). These intermediate cells are just outside the undifferentiated strial epithelium (the black arrowhead in N points to the immature marginal cell layer in hb/hb , see also Figure S1 ). No difference in Kcnj10 expression is detected in Hmx3 KO /Hmx3 KO at this stage compared to control littermates (arrowhead in O), consistent with their EP values being close to normal. Boxes delimit regions in higher magnification. Scale bars: A–E: 20 µm; G,I: 10 µm; J–O; 20 µm. bc: basal cells, bv: blood vessels, ic: intermediate cells, imc: immature marginal cells, isv: immature stria vascularis, oc: organ of Corti, rc: root cell processes, Rm: Reissner's membrane, sp: spiral prominence, sv: stria vascularis.
    Figure Legend Snippet: A–E: Trp2 expression performed on inner ear sagittal sections in hb/hb, Hmx3 KO /Hmx3 KO and control littermates at E12.5 and E16.5. A–C : Trp2 marks neural crest-derived melanoblasts at E12.5 (arrowheads in A). As shown by the arrowheads in B and C, we detect melanoblasts migrating from the neural crest to developing stria is detected in hb/hb , Hmx3 KO /Hmx3 KO , and littermate controls. D–E: While in control mice at E16.5 some intermediate cells precursors are already in the process of interdigitation in the developing stria vascularis (arrowheads in D), none are in the same process in the hb/hb mutants with only a couple of them lying outside the epithelium (arrowheads E). Moreover, Hematoxylin and Eosin counterstaining shows that the epithelium of developing stria looks immature in hb/hb compared to littermate controls (arrows in D,E). Scale bars: 10 µm. F : Cartoon of the cellular structure of stria vascularis. Adapted from [77] . G–I : Immunohistochemistry showing Laminin expression in cochlea and general cochlear morphology of hb/hb, Hmx3 KO /Hmx3 KO and control littermates at P5. Laminin is expressed in all cochlear basal lamina [63] , including stria vascularis, Reissner's membrane, root cell processes and spiral prominence (arrows in G). J–L : Laminin expression in stria vascularis of hb/hb, Hmx3 KO /Hmx3 KO and control littermates at P5. At this stage, we detect basal lamina in blood vessel endothelia (arrowhead in J) and in very small pockets below marginal cells (black arrowhead in J) in control mice. In hb/hb we detect a much stronger laminin expression (denser basal lamina) around the immature stria vascularis (arrow in K). Moreover, we observe fewer and smaller blood vessels in hb/hb compared to littermate controls (examples of blood vessels are labeled with transparent arrowheads in J,K,L). We did not detect any difference in laminin expression in Hmx3 KO /Hmx3 KO compared to littermate controls (arrowhead in L). M–O : Kcnj10 expression in the stria vascularis of hb/hb, Hmx3 KO mutants and control littermates at P5. Kcnj10 is an inward potassium channel of intermediate cells. We detect only some intermediate cells in hb/hb mutants (arrowheads in N) compared to their littermate controls at this stage (M). These intermediate cells are just outside the undifferentiated strial epithelium (the black arrowhead in N points to the immature marginal cell layer in hb/hb , see also Figure S1 ). No difference in Kcnj10 expression is detected in Hmx3 KO /Hmx3 KO at this stage compared to control littermates (arrowhead in O), consistent with their EP values being close to normal. Boxes delimit regions in higher magnification. Scale bars: A–E: 20 µm; G,I: 10 µm; J–O; 20 µm. bc: basal cells, bv: blood vessels, ic: intermediate cells, imc: immature marginal cells, isv: immature stria vascularis, oc: organ of Corti, rc: root cell processes, Rm: Reissner's membrane, sp: spiral prominence, sv: stria vascularis.

    Techniques Used: Expressing, Derivative Assay, Mouse Assay, Immunohistochemistry, Labeling

    The headbobber stria vascularis remains immature with lack of intermediate cells and impaired basal lamina degradation. A–D: Trp2 expression in the vestibular system at E16.5 is analysed by immunohistochemistry in the hb/hb and control littermates on sagittal sections. At this stage, melanoblasts have already reached all the different vestibular structures (arrowheads in B, see E). We can still detect amelanoblasts in hb/hb vestibular system (arrowheads in D). Scale bars: A,C: 100 µm; B,D: 20 µm. Boxes delimit regions in higher magnification. E: Schematic drawings of the flattened vestibular membranes of normally pigmented mice showing distribution of melanocytes in the vestibule viewed on medial (E1) and lateral (E2) position, adapted from [7] . F: Quantitative real-time PCR on cDNA generated from RNA from E12.5 littermate embryo half heads. Netrin-1 mRNA levels are significantly lower in hb/hb than in littermate controls. Error bars, s.d. Quantity normalised to Hprt1 levels. N = 3. **: p
    Figure Legend Snippet: The headbobber stria vascularis remains immature with lack of intermediate cells and impaired basal lamina degradation. A–D: Trp2 expression in the vestibular system at E16.5 is analysed by immunohistochemistry in the hb/hb and control littermates on sagittal sections. At this stage, melanoblasts have already reached all the different vestibular structures (arrowheads in B, see E). We can still detect amelanoblasts in hb/hb vestibular system (arrowheads in D). Scale bars: A,C: 100 µm; B,D: 20 µm. Boxes delimit regions in higher magnification. E: Schematic drawings of the flattened vestibular membranes of normally pigmented mice showing distribution of melanocytes in the vestibule viewed on medial (E1) and lateral (E2) position, adapted from [7] . F: Quantitative real-time PCR on cDNA generated from RNA from E12.5 littermate embryo half heads. Netrin-1 mRNA levels are significantly lower in hb/hb than in littermate controls. Error bars, s.d. Quantity normalised to Hprt1 levels. N = 3. **: p

    Techniques Used: Expressing, Immunohistochemistry, Mouse Assay, Real-time Polymerase Chain Reaction, Generated

    21) Product Images from "Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro – a potential pathway affecting proliferation"

    Article Title: Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro – a potential pathway affecting proliferation

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-20430-0

    Venn diagram of statistically significant differentially expressed genes in BLM-, EXT5 and EXT9-treated mice. Distal lung tissue from mice subjected to s.c. administrations of BLM in combination with p.o. treatment with EXT5, EXT9 or saline was isolated for RNA. With whole genome gene expression array and SAM analysis, significant differentially expressed genes were identified, in comparison to healthy saline controls. p
    Figure Legend Snippet: Venn diagram of statistically significant differentially expressed genes in BLM-, EXT5 and EXT9-treated mice. Distal lung tissue from mice subjected to s.c. administrations of BLM in combination with p.o. treatment with EXT5, EXT9 or saline was isolated for RNA. With whole genome gene expression array and SAM analysis, significant differentially expressed genes were identified, in comparison to healthy saline controls. p

    Techniques Used: Mouse Assay, Isolation, Expressing

    22) Product Images from "Targeting glioma stem‐like cell survival and chemoresistance through inhibition of lysine‐specific histone demethylase KDM2B"

    Article Title: Targeting glioma stem‐like cell survival and chemoresistance through inhibition of lysine‐specific histone demethylase KDM2B

    Journal: Molecular Oncology

    doi: 10.1002/1878-0261.12174

    si RNA ‐mediated knockdown of KDM 2B impairs glioblastoma cell viability and proliferation. (A) Immunoblot analysis of KDM 2B and GAPDH (loading control) in glioblastoma cells compared to normal human astrocytes ( NHA ). (B) Immunoblot analysis of KDM 2B and tubulin (loading control) in tissue extracts from glioblastoma samples compared to normal brain ( NB ). (C) qRT / PCR analysis of relative KDM 2B mRNA expression in glioblastoma cells 48 h post‐transfection with either si CTRL or two independent si RNA constructs targeting KDM 2B (si KDM 2B‐1 and si KDM 2B‐2). Data are presented as mean ± SEM , n = 4. ** P
    Figure Legend Snippet: si RNA ‐mediated knockdown of KDM 2B impairs glioblastoma cell viability and proliferation. (A) Immunoblot analysis of KDM 2B and GAPDH (loading control) in glioblastoma cells compared to normal human astrocytes ( NHA ). (B) Immunoblot analysis of KDM 2B and tubulin (loading control) in tissue extracts from glioblastoma samples compared to normal brain ( NB ). (C) qRT / PCR analysis of relative KDM 2B mRNA expression in glioblastoma cells 48 h post‐transfection with either si CTRL or two independent si RNA constructs targeting KDM 2B (si KDM 2B‐1 and si KDM 2B‐2). Data are presented as mean ± SEM , n = 4. ** P

    Techniques Used: Quantitative RT-PCR, Expressing, Transfection, Construct

    23) Product Images from "Adenovirus Type 5 Rupture of Lysosomes Leads to Cathepsin B-Dependent Mitochondrial Stress and Production of Reactive Oxygen Species ▿"

    Article Title: Adenovirus Type 5 Rupture of Lysosomes Leads to Cathepsin B-Dependent Mitochondrial Stress and Production of Reactive Oxygen Species ▿

    Journal: Journal of Virology

    doi: 10.1128/JVI.00675-11

    ROS production in response to Ad5 in the presence or absence of gp91phox (Nox2) knockdown. (A) RNA was isolated from THP-1 control cells and THP-1-gp91phox knockdown cells, and subjected to qRT-PCR using primer sets for gp91phox and β-actin. Relative gp91phox expression was generated using the 2 −ΔΔ CT method where the fold change in gp91phox expression was normalized to the housekeeping gene β-actin and gp91phox expression in the THP-1 control cells is set to 1. (B) PMA-differentiated THP-1 control cells (white bars) and THP-1-gp91phox knockdown cells (black bars) were serum starved for 3 h then incubated with 10 μM DCFDA for 30 min, washed, and left untreated, treated with Ad5 at 100,000 ppc, or treated with 5 mM ATP. DCF fluorescence was measured on a fluorescent plate reader. Graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. Significance was determined by Student's t test (unpaired), where * indicates P
    Figure Legend Snippet: ROS production in response to Ad5 in the presence or absence of gp91phox (Nox2) knockdown. (A) RNA was isolated from THP-1 control cells and THP-1-gp91phox knockdown cells, and subjected to qRT-PCR using primer sets for gp91phox and β-actin. Relative gp91phox expression was generated using the 2 −ΔΔ CT method where the fold change in gp91phox expression was normalized to the housekeeping gene β-actin and gp91phox expression in the THP-1 control cells is set to 1. (B) PMA-differentiated THP-1 control cells (white bars) and THP-1-gp91phox knockdown cells (black bars) were serum starved for 3 h then incubated with 10 μM DCFDA for 30 min, washed, and left untreated, treated with Ad5 at 100,000 ppc, or treated with 5 mM ATP. DCF fluorescence was measured on a fluorescent plate reader. Graph depicts relative fluorescence intensity at 6 h postinfection normalized to time zero. Significance was determined by Student's t test (unpaired), where * indicates P

    Techniques Used: Isolation, Quantitative RT-PCR, Expressing, Generated, Incubation, Fluorescence

    24) Product Images from "NS-398, Ibuprofen and COX-2 RNAi produce significantly different gene expression profiles in prostate cancer cells"

    Article Title: NS-398, Ibuprofen and COX-2 RNAi produce significantly different gene expression profiles in prostate cancer cells

    Journal: Molecular cancer therapeutics

    doi: 10.1158/1535-7163.MCT-08-0928

    Venn diagrams showing the number of overlapping genes in comparison of 0.01mM NS-398, 0.1mM ibuprofen and siCOX-2 (A, B); and 0.1mM NS-398, 1.5mM ibuprofen and siCOX-2 (C, D). A and C: - up regulated genes, B and D: - down regulated genes. The number
    Figure Legend Snippet: Venn diagrams showing the number of overlapping genes in comparison of 0.01mM NS-398, 0.1mM ibuprofen and siCOX-2 (A, B); and 0.1mM NS-398, 1.5mM ibuprofen and siCOX-2 (C, D). A and C: - up regulated genes, B and D: - down regulated genes. The number

    Techniques Used:

    25) Product Images from "RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition"

    Article Title: RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0121659

    Analysis of technical bias to perceived community composition. (A) NMDS of the 16S rRNA gene amplicon sequencing data based on a Bray-Curtis dissimilarity matrix generated after random subsampling of 2,800 sequences from each sample. Bars indicate the range of coordinates for the three replicate extractions/sequencing datasets per treatment. (B) Phylum level data (top 10 most abundant phyla, fractions of all reads). Number 1–3 between parentheses indicates the sequencing run from which each dataset is derived. APO combines three slightly different treatments that did not result in significantly different taxonomic representations ( S2 Fig .). Acronyms: Extraction protocols: APS (standard AllPrep protocol), APO (optimized AllPrep protocol), Enz (Enzymatic protocol), Bead (Bead-beating protocol); Preservation methods: NT (none), RL (RNAlater), RP (RNAprotect), BU (Qiagen Lysis Buffer RLT+); Other modifications: LYS (lysozyme), NQ (No QIAshredder column), TL (bead-beating with TissueLyser). Except for the APO samples, none of the Douglas Lake filters were preserved in RNA protection agents.
    Figure Legend Snippet: Analysis of technical bias to perceived community composition. (A) NMDS of the 16S rRNA gene amplicon sequencing data based on a Bray-Curtis dissimilarity matrix generated after random subsampling of 2,800 sequences from each sample. Bars indicate the range of coordinates for the three replicate extractions/sequencing datasets per treatment. (B) Phylum level data (top 10 most abundant phyla, fractions of all reads). Number 1–3 between parentheses indicates the sequencing run from which each dataset is derived. APO combines three slightly different treatments that did not result in significantly different taxonomic representations ( S2 Fig .). Acronyms: Extraction protocols: APS (standard AllPrep protocol), APO (optimized AllPrep protocol), Enz (Enzymatic protocol), Bead (Bead-beating protocol); Preservation methods: NT (none), RL (RNAlater), RP (RNAprotect), BU (Qiagen Lysis Buffer RLT+); Other modifications: LYS (lysozyme), NQ (No QIAshredder column), TL (bead-beating with TissueLyser). Except for the APO samples, none of the Douglas Lake filters were preserved in RNA protection agents.

    Techniques Used: Amplification, Sequencing, Generated, Derivative Assay, Preserving, Lysis

    26) Product Images from "Fabricating retinal pigment epithelial cell sheets derived from human induced pluripotent stem cells in an automated closed culture system for regenerative medicine"

    Article Title: Fabricating retinal pigment epithelial cell sheets derived from human induced pluripotent stem cells in an automated closed culture system for regenerative medicine

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0212369

    Real-time PCR analysis of RPE-related gene expression in hiPS-RPE cell sheets. Data were obtained from two independent experiments. Machine cell culture, n = 7, manual cell culture, n = 5. All data are represented as the means ± SD.
    Figure Legend Snippet: Real-time PCR analysis of RPE-related gene expression in hiPS-RPE cell sheets. Data were obtained from two independent experiments. Machine cell culture, n = 7, manual cell culture, n = 5. All data are represented as the means ± SD.

    Techniques Used: Real-time Polymerase Chain Reaction, Expressing, Cell Culture

    27) Product Images from "Simvastatin induces cell cycle arrest and inhibits proliferation of bladder cancer cells via PPARγ signalling pathway"

    Article Title: Simvastatin induces cell cycle arrest and inhibits proliferation of bladder cancer cells via PPARγ signalling pathway

    Journal: Scientific Reports

    doi: 10.1038/srep35783

    Transcriptome profiling of bladder cancer compared to normal bladder tissues pointed out the PPAR family. ( a ) Heat map of the differentially expressed genes in three bladder cancer tissues compared with three normal bladder tissues. Red color indicated upregulated genes and green color indicated downregulated genes. ( b ) GO-map network analysis by GCBI platform revealed fatty acid biosynthesis and glycerolipid metabolism were linked with bladder cancer via PPAR and ErbB signalling pathways, as well as a close correlation between bladder cancer and cell cycle. ( c ) Semiquantitative RT-PCR analysis for alterations of PPAR family ( PPARα , PPARβ and PPAR γ) using pooled total RNA isolated from the three bladder cancer tissues versus three normal bladder tissues. The expression of the GAPDH mRNA was used as a loading control. ( d ) ELISA analysis revealed the relative PPARγ DNA-binding activity in the BCa tissues was significantly decreased comparing with the normal bladder tissues (n = 3). *p
    Figure Legend Snippet: Transcriptome profiling of bladder cancer compared to normal bladder tissues pointed out the PPAR family. ( a ) Heat map of the differentially expressed genes in three bladder cancer tissues compared with three normal bladder tissues. Red color indicated upregulated genes and green color indicated downregulated genes. ( b ) GO-map network analysis by GCBI platform revealed fatty acid biosynthesis and glycerolipid metabolism were linked with bladder cancer via PPAR and ErbB signalling pathways, as well as a close correlation between bladder cancer and cell cycle. ( c ) Semiquantitative RT-PCR analysis for alterations of PPAR family ( PPARα , PPARβ and PPAR γ) using pooled total RNA isolated from the three bladder cancer tissues versus three normal bladder tissues. The expression of the GAPDH mRNA was used as a loading control. ( d ) ELISA analysis revealed the relative PPARγ DNA-binding activity in the BCa tissues was significantly decreased comparing with the normal bladder tissues (n = 3). *p

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Isolation, Expressing, Enzyme-linked Immunosorbent Assay, Binding Assay, Activity Assay, BIA-KA

    28) Product Images from "Tuning of mRNA stability through altering 3′-UTR sequences generates distinct output expression in a synthetic circuit driven by p53 oscillations"

    Article Title: Tuning of mRNA stability through altering 3′-UTR sequences generates distinct output expression in a synthetic circuit driven by p53 oscillations

    Journal: Scientific Reports

    doi: 10.1038/s41598-019-42509-y

    Distinct naturally occurring 3′-UTRs confer different output transcript stabilities to generate different expression dynamics of mCherry expression induced by p53 oscillations. ( A ) Schematic of the synthetic circuit with output reporter constructs with DDB2 , TRIAP1 or GADD45A 3′-UTR inserted following the mCherry coding sequence. Predicted phenotype for output mCherry expression in individual cells. ( B – D ) mRNA decay rates of mCherry transcripts with the DDB2 ( B ), TRIAP1 ( C ), or GADD45A ( D ) 3′-UTR. All data are normalized by GAPDH transcript levels. Data are mean values ± SEM for 5 biological replicates. ( E – J ) mCherry expression in single cells following NCS treatment to induce p53 oscillations in cells containing DDB2 ( E , F ), TRIAP1 ( G , H ), or GADD45A ( I , J ) 3′-UTR for the mCherry output transcript. Gray lines represent mean nuclear mCherry expression in individual cells, red lines represent mean of the population for all cells in each condition ( E , G , I ). Representative single cell traces are shown in ( F , H , J ). Approximately 50 cells were quantified per condition.
    Figure Legend Snippet: Distinct naturally occurring 3′-UTRs confer different output transcript stabilities to generate different expression dynamics of mCherry expression induced by p53 oscillations. ( A ) Schematic of the synthetic circuit with output reporter constructs with DDB2 , TRIAP1 or GADD45A 3′-UTR inserted following the mCherry coding sequence. Predicted phenotype for output mCherry expression in individual cells. ( B – D ) mRNA decay rates of mCherry transcripts with the DDB2 ( B ), TRIAP1 ( C ), or GADD45A ( D ) 3′-UTR. All data are normalized by GAPDH transcript levels. Data are mean values ± SEM for 5 biological replicates. ( E – J ) mCherry expression in single cells following NCS treatment to induce p53 oscillations in cells containing DDB2 ( E , F ), TRIAP1 ( G , H ), or GADD45A ( I , J ) 3′-UTR for the mCherry output transcript. Gray lines represent mean nuclear mCherry expression in individual cells, red lines represent mean of the population for all cells in each condition ( E , G , I ). Representative single cell traces are shown in ( F , H , J ). Approximately 50 cells were quantified per condition.

    Techniques Used: Expressing, Construct, Sequencing

    Restoration of apoptotic activity in a tunable synthetic circuit driven by p53 oscillations. ( A ) Schematic of the synthetic circuit with caspase-3 output constructs with DDB2 , TRIAP1 or GADD45A 3′-UTR inserted following the CASP3 coding sequence. Predicted phenotype for apoptosis in individual cells. (B-D) mRNA decay rates of CASP3 transcripts with the DDB2 ( B ), TRIAP1 ( C ), or GADD45A ( D ) 3′-UTR. All data are normalized by GAPDH transcript levels. Data are mean values ± SEM for 3 ( B ) or 5 ( C , D ) biological replicates. ( E ) Fold changes in the number of late apoptotic cells 24 h after NCS treatment for cells expression CASP3 with different 3′-UTRs. Data represent mean ± SEM for triplicate experiments. (*indicates statistically significant difference, p
    Figure Legend Snippet: Restoration of apoptotic activity in a tunable synthetic circuit driven by p53 oscillations. ( A ) Schematic of the synthetic circuit with caspase-3 output constructs with DDB2 , TRIAP1 or GADD45A 3′-UTR inserted following the CASP3 coding sequence. Predicted phenotype for apoptosis in individual cells. (B-D) mRNA decay rates of CASP3 transcripts with the DDB2 ( B ), TRIAP1 ( C ), or GADD45A ( D ) 3′-UTR. All data are normalized by GAPDH transcript levels. Data are mean values ± SEM for 3 ( B ) or 5 ( C , D ) biological replicates. ( E ) Fold changes in the number of late apoptotic cells 24 h after NCS treatment for cells expression CASP3 with different 3′-UTRs. Data represent mean ± SEM for triplicate experiments. (*indicates statistically significant difference, p

    Techniques Used: Activity Assay, Construct, Sequencing, Expressing

    An oscillating transcription factor generates distinct output expression dynamics as a function of mRNA decay rates. A model predicts that distinct mRNA and protein expression dynamics can be generated by altering the transcript stability of target genes induced by an oscillating transcription factor. 3′-UTRs can confer different transcript stabilities. Based on the relationship between the transcript decay rate and the oscillator frequency, output gene transcripts will have rising, weakly pulsing, or strongly pulsing mRNA expression dynamics, leading to alterations in the rate of accumulation of an output protein product.
    Figure Legend Snippet: An oscillating transcription factor generates distinct output expression dynamics as a function of mRNA decay rates. A model predicts that distinct mRNA and protein expression dynamics can be generated by altering the transcript stability of target genes induced by an oscillating transcription factor. 3′-UTRs can confer different transcript stabilities. Based on the relationship between the transcript decay rate and the oscillator frequency, output gene transcripts will have rising, weakly pulsing, or strongly pulsing mRNA expression dynamics, leading to alterations in the rate of accumulation of an output protein product.

    Techniques Used: Expressing, Generated

    29) Product Images from "Pitpnm1 is expressed in hair cells during development but is not required for hearing "

    Article Title: Pitpnm1 is expressed in hair cells during development but is not required for hearing

    Journal: Neuroscience

    doi: 10.1016/j.neuroscience.2013.06.045

    Organ of Corti RT-PCR for Pitpnm genes. RT-PCR results showing bands for Pitpnm1 (left), Pitpnm2 (centre) and Pitpnm3 (right) from cDNA from the organ of Corti of three separate mice (A–C). Ladder band size is shown on each figure; the Pitpnm bands are between 200 and 350 bp in size.
    Figure Legend Snippet: Organ of Corti RT-PCR for Pitpnm genes. RT-PCR results showing bands for Pitpnm1 (left), Pitpnm2 (centre) and Pitpnm3 (right) from cDNA from the organ of Corti of three separate mice (A–C). Ladder band size is shown on each figure; the Pitpnm bands are between 200 and 350 bp in size.

    Techniques Used: Reverse Transcription Polymerase Chain Reaction, Mouse Assay

    30) Product Images from "Wbp2 is required for normal glutamatergic synapses in the cochlea and is crucial for hearing"

    Article Title: Wbp2 is required for normal glutamatergic synapses in the cochlea and is crucial for hearing

    Journal: EMBO Molecular Medicine

    doi: 10.15252/emmm.201505523

    GluR2/3 expression and synaptic defects in Wbp2‐deficient mice We arrayed synapse images aligned by ascending size of the post‐synaptic site after GluR2/3 and Ct BP 2 labelling. This is a composite image made of several synapses taken from a single IHC from a single wt and a single hom, representing double labelling experiments performed on 3 mutants and 3 controls. Synapses in the mutants show abnormal morphology and smaller green patches, suggesting reduced expression of the GluR2/3 AMPA receptor subunits. Scale bar (shown on the bottom right), 1 μm. TEM images of IHC ribbon synapses of wt (B, arrowheads for synaptic vesicles) and homs (C–G) at 4 weeks of age, showing a representative array of synaptic phenotypes in the 24‐ kH z cochlear region of mutants. While in (C) and (D) the ribbons look slightly abnormal in size with misplaced synaptic vesicles (arrowheads in C), we also observe orphan post‐synaptic densities surrounded by floating synaptic vesicles (arrowheads in E); ribbons with synaptic membranes (arrow in F) that have detached from the IHC membrane (the arrowhead labels the original position of the synapse before detachment) and are floating in the swollen nerve terminal (F); ribbons (arrow in G) that are detached from their densities (arrowhead in G). Scale bars: (B–E), 200 nm; (F, G), 500 nm. nt: nerve terminal; psd: post‐synaptic density; snt: swollen nerve terminal. Source data are available online for this figure.
    Figure Legend Snippet: GluR2/3 expression and synaptic defects in Wbp2‐deficient mice We arrayed synapse images aligned by ascending size of the post‐synaptic site after GluR2/3 and Ct BP 2 labelling. This is a composite image made of several synapses taken from a single IHC from a single wt and a single hom, representing double labelling experiments performed on 3 mutants and 3 controls. Synapses in the mutants show abnormal morphology and smaller green patches, suggesting reduced expression of the GluR2/3 AMPA receptor subunits. Scale bar (shown on the bottom right), 1 μm. TEM images of IHC ribbon synapses of wt (B, arrowheads for synaptic vesicles) and homs (C–G) at 4 weeks of age, showing a representative array of synaptic phenotypes in the 24‐ kH z cochlear region of mutants. While in (C) and (D) the ribbons look slightly abnormal in size with misplaced synaptic vesicles (arrowheads in C), we also observe orphan post‐synaptic densities surrounded by floating synaptic vesicles (arrowheads in E); ribbons with synaptic membranes (arrow in F) that have detached from the IHC membrane (the arrowhead labels the original position of the synapse before detachment) and are floating in the swollen nerve terminal (F); ribbons (arrow in G) that are detached from their densities (arrowhead in G). Scale bars: (B–E), 200 nm; (F, G), 500 nm. nt: nerve terminal; psd: post‐synaptic density; snt: swollen nerve terminal. Source data are available online for this figure.

    Techniques Used: Expressing, Mouse Assay, Immunohistochemistry, Transmission Electron Microscopy

    Afferent innervation in Wbp2‐deficient mice At P14, afferent terminals below IHC s are slightly swollen in the mutants (neurofilament labelling in green, arrowheads to compare; Ct BP 2 labels ribbons and IHC nuclei in red). Scale bars, 10 μm. At P28, neurofilament/Ct BP 2 labelling in the organ of Corti of 4‐week‐old Wbp2‐deficient mice and littermate controls shows severe swelling of IHC afferent terminals in the mutants, especially in the 24‐ kH z region (yellow arrowheads). The pre‐synaptic ribbons do not look as well aligned to the terminals in the mutants (white arrows). At this stage, we also observe swelling of OHC afferent terminals in the 24‐ kH z region (empty arrowheads). Scale bars, 5 μm. ihc: IHC nucleus; p: pillar side; m: modiolar side. Counts of pre‐synaptic ribbons per IHC in the 8‐, 18‐ and 24‐ kH z regions, showing no difference between mutants and controls at P28. TEM of the organ of Corti performed at P28 showing swollen afferent terminals below inner and outer hair cells (arrowheads for comparisons between mutants and controls). Scale bars, 5 μm. Neurofilament/Ct BP 2 labelling shows swollen and retracting terminals (white arrows), especially in the 24‐ kH z regions in the mutants at 8 weeks (arrows). Scale bars, 10 μm. Counts of pre‐synaptic ribbons in the 8‐, 18‐ and 24‐ kH z regions, showing no difference in their number per IHC in the mutants compared to littermate controls at 8 weeks. Data information: All data are shown as mean ± SD and statistically analysed by two‐tailed Student's t ‐test. n = 35 hair cells. Synaptic count at 4 weeks: wild type : 24 kH z 16.9 ± 2.4, 16 kH z 13.67 ± 2, 9 kH z 13.0 ± 1.8; mutants: 24 kH z 18.17 ± 1.18 ( P = 0.27), 16 kH z 15.89 ± 1.8 ( P = 0.26), 9 kH z 15 ± 2 ( P = 0.07). Synaptic count at 8 weeks: wild type: 24 kH z: 15.35 ± 3.75, 18 kH z 17.73 ± 1.79, 8 kH z: 11.25 ± 0.92; mutants: 24 kH z: 15.78 ± 3.46 ( P = 0.9), 18 kH z 15.78 ± 0.17 ( P = 0.26), 8 kH z: 12.3 ± 2.26 ( P = 0.6) Source data are available online for this figure.
    Figure Legend Snippet: Afferent innervation in Wbp2‐deficient mice At P14, afferent terminals below IHC s are slightly swollen in the mutants (neurofilament labelling in green, arrowheads to compare; Ct BP 2 labels ribbons and IHC nuclei in red). Scale bars, 10 μm. At P28, neurofilament/Ct BP 2 labelling in the organ of Corti of 4‐week‐old Wbp2‐deficient mice and littermate controls shows severe swelling of IHC afferent terminals in the mutants, especially in the 24‐ kH z region (yellow arrowheads). The pre‐synaptic ribbons do not look as well aligned to the terminals in the mutants (white arrows). At this stage, we also observe swelling of OHC afferent terminals in the 24‐ kH z region (empty arrowheads). Scale bars, 5 μm. ihc: IHC nucleus; p: pillar side; m: modiolar side. Counts of pre‐synaptic ribbons per IHC in the 8‐, 18‐ and 24‐ kH z regions, showing no difference between mutants and controls at P28. TEM of the organ of Corti performed at P28 showing swollen afferent terminals below inner and outer hair cells (arrowheads for comparisons between mutants and controls). Scale bars, 5 μm. Neurofilament/Ct BP 2 labelling shows swollen and retracting terminals (white arrows), especially in the 24‐ kH z regions in the mutants at 8 weeks (arrows). Scale bars, 10 μm. Counts of pre‐synaptic ribbons in the 8‐, 18‐ and 24‐ kH z regions, showing no difference in their number per IHC in the mutants compared to littermate controls at 8 weeks. Data information: All data are shown as mean ± SD and statistically analysed by two‐tailed Student's t ‐test. n = 35 hair cells. Synaptic count at 4 weeks: wild type : 24 kH z 16.9 ± 2.4, 16 kH z 13.67 ± 2, 9 kH z 13.0 ± 1.8; mutants: 24 kH z 18.17 ± 1.18 ( P = 0.27), 16 kH z 15.89 ± 1.8 ( P = 0.26), 9 kH z 15 ± 2 ( P = 0.07). Synaptic count at 8 weeks: wild type: 24 kH z: 15.35 ± 3.75, 18 kH z 17.73 ± 1.79, 8 kH z: 11.25 ± 0.92; mutants: 24 kH z: 15.78 ± 3.46 ( P = 0.9), 18 kH z 15.78 ± 0.17 ( P = 0.26), 8 kH z: 12.3 ± 2.26 ( P = 0.6) Source data are available online for this figure.

    Techniques Used: Mouse Assay, Immunohistochemistry, Transmission Electron Microscopy, Two Tailed Test

    Wbp2 mutation and Wbp2 expression in the cochlea Diagram showing the design of the mutated Wbp2 allele. A promoterless cassette including LacZ and neo genes was inserted in the second intron of the Wbp2 gene flanked by FRT sites (green triangles). LoxP sites (red triangles) flank the critical exon (exon 2) of the Wbp2 gene (exons in yellow). Western blot showing no detectable Wbp2 protein in 4‐week‐old mutant brain compared to wt littermate controls; 5 μg of the protein lysate was subjected to 10% SDS – PAGE . β‐tubulin was used as a loading control. Wbp2 l and Wbp2 s refer to the long and short isoforms, respectively. Quantitative real‐time PCR showing severe knockdown of Wbp2 transcription in 4‐week‐old mutant ( n = 3) inner ears and eyes, compared to wt littermate controls ( n = 3). Heterozygotes show intermediate levels. Hprt was used as a control and levels are normalised to wt levels. Data plotted as mean ± SD . Two‐tailed t ‐test: Wbp2 ear: het * P = 0.03, hom *** P = 0.000000033; Wbp2 eye: het * P = 0.01, hom *** P = 5.35537E‐13. X‐gal staining of Wbp2 hets at P14 showing Wbp2 expression (blue) in all the main cochlear structures: the stria vascularis (black arrowhead in D), spiral prominence (empty arrowhead in D), Reissner's membrane (arrow in D), strong expression in the spiral ganglion cells (arrowheads in E) and in IHC s and OHC s in the organ of Corti (arrowheads in F). Scale bars: (D), 50 μm; (E, F), 20 μm. ihc: inner hair cells; ohc: outer hair cells. No X‐gal staining is observed in wt controls (not shown). The X‐gal reaction is always cytoplasmic. Source data are available online for this figure.
    Figure Legend Snippet: Wbp2 mutation and Wbp2 expression in the cochlea Diagram showing the design of the mutated Wbp2 allele. A promoterless cassette including LacZ and neo genes was inserted in the second intron of the Wbp2 gene flanked by FRT sites (green triangles). LoxP sites (red triangles) flank the critical exon (exon 2) of the Wbp2 gene (exons in yellow). Western blot showing no detectable Wbp2 protein in 4‐week‐old mutant brain compared to wt littermate controls; 5 μg of the protein lysate was subjected to 10% SDS – PAGE . β‐tubulin was used as a loading control. Wbp2 l and Wbp2 s refer to the long and short isoforms, respectively. Quantitative real‐time PCR showing severe knockdown of Wbp2 transcription in 4‐week‐old mutant ( n = 3) inner ears and eyes, compared to wt littermate controls ( n = 3). Heterozygotes show intermediate levels. Hprt was used as a control and levels are normalised to wt levels. Data plotted as mean ± SD . Two‐tailed t ‐test: Wbp2 ear: het * P = 0.03, hom *** P = 0.000000033; Wbp2 eye: het * P = 0.01, hom *** P = 5.35537E‐13. X‐gal staining of Wbp2 hets at P14 showing Wbp2 expression (blue) in all the main cochlear structures: the stria vascularis (black arrowhead in D), spiral prominence (empty arrowhead in D), Reissner's membrane (arrow in D), strong expression in the spiral ganglion cells (arrowheads in E) and in IHC s and OHC s in the organ of Corti (arrowheads in F). Scale bars: (D), 50 μm; (E, F), 20 μm. ihc: inner hair cells; ohc: outer hair cells. No X‐gal staining is observed in wt controls (not shown). The X‐gal reaction is always cytoplasmic. Source data are available online for this figure.

    Techniques Used: Mutagenesis, Expressing, Western Blot, SDS Page, Real-time Polymerase Chain Reaction, Two Tailed Test, Staining, Immunohistochemistry

    Analysis of the Wbp2 mouse isoforms in the brain and in the cochlea Splice forms of WBP 2 , numbered according to the Ensembl numbering scheme. The GRAM domain is marked in blue, the WW domains in green and the locations of the variants in black (the p.Ala160Thr and p.Met163Leu variants are too close to show separately in this view). Agarose gel trace of cDNA obtained from mouse wt P28 inner ear ( IE ), P28 brain, adult and P4 organ of Corti ( OC ). Results show the expression of two Wbp2 isoforms in the brain at P28 and very faint band for the short isoform together with a strong band for the long isoform in the inner ear at P28. If we look at just the organ of Corti (adult and P4), we observe a strong band for the long isoform in the P4 OC and an almost undetectable band for the short isoform, which was not even picked up by sequencing (see C). Wbp2 l: long isoform (550 bp); Wbp2 s: short isoform (480 bp). Cartoon illustrating the results from the sequencing of mouse wt cDNA performed at P4 and P28. While in the brain we detect both Wbp2 isoforms and in the organ of Corti only the long isoform, in the whole inner ear sample we detect the presence of the long isoform with a small band for the short one. Western blot showing the predominant presence of the Wbp2 long isoform in the cochlea at P28, with a weak trace of the short isoform showing up only when a higher concentration of protein lysate (20 μg) is loaded. Both isoforms are absent in the Wbp2‐deficient mouse. Gapdh was used as a loading control. Wbp2 l: long isoform; Wbp2 s: short isoform. Source data are available online for this figure.
    Figure Legend Snippet: Analysis of the Wbp2 mouse isoforms in the brain and in the cochlea Splice forms of WBP 2 , numbered according to the Ensembl numbering scheme. The GRAM domain is marked in blue, the WW domains in green and the locations of the variants in black (the p.Ala160Thr and p.Met163Leu variants are too close to show separately in this view). Agarose gel trace of cDNA obtained from mouse wt P28 inner ear ( IE ), P28 brain, adult and P4 organ of Corti ( OC ). Results show the expression of two Wbp2 isoforms in the brain at P28 and very faint band for the short isoform together with a strong band for the long isoform in the inner ear at P28. If we look at just the organ of Corti (adult and P4), we observe a strong band for the long isoform in the P4 OC and an almost undetectable band for the short isoform, which was not even picked up by sequencing (see C). Wbp2 l: long isoform (550 bp); Wbp2 s: short isoform (480 bp). Cartoon illustrating the results from the sequencing of mouse wt cDNA performed at P4 and P28. While in the brain we detect both Wbp2 isoforms and in the organ of Corti only the long isoform, in the whole inner ear sample we detect the presence of the long isoform with a small band for the short one. Western blot showing the predominant presence of the Wbp2 long isoform in the cochlea at P28, with a weak trace of the short isoform showing up only when a higher concentration of protein lysate (20 μg) is loaded. Both isoforms are absent in the Wbp2‐deficient mouse. Gapdh was used as a loading control. Wbp2 l: long isoform; Wbp2 s: short isoform. Source data are available online for this figure.

    Techniques Used: Agarose Gel Electrophoresis, Expressing, Sequencing, Western Blot, Concentration Assay

    The Wbp2 molecular pathway Diagram showing the Wbp2 molecular pathway, including its downstream targets and their functional relationship. The blue arrows, light blue lines and green lines link data from the literature ( in vivo and in vitro ); the orange squares and red arrows indicate up‐ or down‐regulation shown in our experimental observations, as reported in this study. Quantitative real‐time PCR showing reduced mRNA levels for Esr1 , Esr2 and Pgr and up‐regulation of Shank3 and Psd‐95 in cochleae of 4‐week‐old Wbp2‐deficient mice compared to littermate controls ( n = 3 for each genotype). Hprt is used as a relative control. *P = 0.03 for Psd‐95; **P = 0.007 for Shank3 ; *P = 0.03 for Esr2 ; **P = 0.0016 for Esr1 ; *P = 0.037 for Pgr . Synapses from one mutant and one control IHC at 4 weeks of age after Psd‐95 and Ct BP 2 labelling, showing stronger Psd‐95 expression in the mutants compared to controls, representing double labelling experiments performed on 3 mutants and 3 controls. Scale bar, 10 μm. Quantification of Psd95 fluorescence in IHC synapses, representing expression in the apical (9‐ kH z best frequency region of the cochlea) and basal (24‐ kH z best frequency region of the cochlea) regions at 4 weeks of age. Data from 2 wt and 2 homs were analysed (16 synapses per cochlear region per mouse). AU , arbitrary units. Wt: 24 kH z 22.41 ± 10.70, 9 kH z 11.045 ± 2.128; mutants: 24 kH z 66.73 ± 13.70, P = 0.069; 9 kH z: 26.02 ± 5.79 P = 0.075. Data information: Data are shown as mean ± SD and were statistically analysed by two‐tailed Student's t ‐test. Source data are available online for this figure.
    Figure Legend Snippet: The Wbp2 molecular pathway Diagram showing the Wbp2 molecular pathway, including its downstream targets and their functional relationship. The blue arrows, light blue lines and green lines link data from the literature ( in vivo and in vitro ); the orange squares and red arrows indicate up‐ or down‐regulation shown in our experimental observations, as reported in this study. Quantitative real‐time PCR showing reduced mRNA levels for Esr1 , Esr2 and Pgr and up‐regulation of Shank3 and Psd‐95 in cochleae of 4‐week‐old Wbp2‐deficient mice compared to littermate controls ( n = 3 for each genotype). Hprt is used as a relative control. *P = 0.03 for Psd‐95; **P = 0.007 for Shank3 ; *P = 0.03 for Esr2 ; **P = 0.0016 for Esr1 ; *P = 0.037 for Pgr . Synapses from one mutant and one control IHC at 4 weeks of age after Psd‐95 and Ct BP 2 labelling, showing stronger Psd‐95 expression in the mutants compared to controls, representing double labelling experiments performed on 3 mutants and 3 controls. Scale bar, 10 μm. Quantification of Psd95 fluorescence in IHC synapses, representing expression in the apical (9‐ kH z best frequency region of the cochlea) and basal (24‐ kH z best frequency region of the cochlea) regions at 4 weeks of age. Data from 2 wt and 2 homs were analysed (16 synapses per cochlear region per mouse). AU , arbitrary units. Wt: 24 kH z 22.41 ± 10.70, 9 kH z 11.045 ± 2.128; mutants: 24 kH z 66.73 ± 13.70, P = 0.069; 9 kH z: 26.02 ± 5.79 P = 0.075. Data information: Data are shown as mean ± SD and were statistically analysed by two‐tailed Student's t ‐test. Source data are available online for this figure.

    Techniques Used: Functional Assay, In Vivo, In Vitro, Real-time Polymerase Chain Reaction, Mouse Assay, Mutagenesis, Immunohistochemistry, Expressing, Fluorescence, Two Tailed Test

    Histology of organ of Corti Semi‐thin sections stained with toluidine blue show no cochlear abnormalities and no obvious loss of spiral ganglion cells in Wbp2‐deficient mice compared to controls at 4 weeks. Scale bar: 20 μm. SG : spiral ganglion cells.
    Figure Legend Snippet: Histology of organ of Corti Semi‐thin sections stained with toluidine blue show no cochlear abnormalities and no obvious loss of spiral ganglion cells in Wbp2‐deficient mice compared to controls at 4 weeks. Scale bar: 20 μm. SG : spiral ganglion cells.

    Techniques Used: Staining, Mouse Assay

    Auditory responses of Wbp2‐deficient mice Mean ABR thresholds (± SD ) for clicks and tone pips are plotted for wt (green), het (blue) and hom (red) mice at ages (A) P14 (wt, n = 3; het, n = 8; hom, n = 6); (B) 4 weeks (wt, n = 38; het, n = 26; hom, n = 37); (C) 14 weeks (wt, n = 10; hom, n = 14); (D) 28 weeks (wt, n = 15; het, n = 5; hom, n = 25); (E) 44 weeks (wt, n = 9; het, n = 2; hom, n = 11). Grey symbols and lines indicate thresholds of individual mutants. In (B), open symbols represent thresholds under urethane anaesthesia (see Materials and Methods ), showing no difference compared with ketamine/xylazine used for all other thresholds. Mean thresholds for mutants aged 2 weeks (yellow), 4 weeks (purple), 14 weeks (cyan), 28 weeks (grey) and 44 weeks (black). Averaged click‐evoked ABR waveforms from 4‐week‐old wt ( n = 23, green) and mutants ( n = 34, red), at 50‐ dB sensation level ( SL ) (left panel). SP and ABR wave 1 (W1) are indicated by grey areas. Expanded averaged SP and ABR W1 waveform patterns for 10‐ to 60‐ dB SL in 10‐ dB increments are plotted in green (wt; middle panel) and red (mutants; right panel), to illustrate the growth of SP and W1 with stimulus level. Mean 2f1‐f2 DPOAE thresholds (± SD ) are plotted for wt (green), heterozygote (blue) and homozygous (red) mice aged 4 weeks (H: wt, n = 5; hom, n = 5) or 21 weeks (I: het, n = 3; hom, n = 5), as a function of f2 frequency.
    Figure Legend Snippet: Auditory responses of Wbp2‐deficient mice Mean ABR thresholds (± SD ) for clicks and tone pips are plotted for wt (green), het (blue) and hom (red) mice at ages (A) P14 (wt, n = 3; het, n = 8; hom, n = 6); (B) 4 weeks (wt, n = 38; het, n = 26; hom, n = 37); (C) 14 weeks (wt, n = 10; hom, n = 14); (D) 28 weeks (wt, n = 15; het, n = 5; hom, n = 25); (E) 44 weeks (wt, n = 9; het, n = 2; hom, n = 11). Grey symbols and lines indicate thresholds of individual mutants. In (B), open symbols represent thresholds under urethane anaesthesia (see Materials and Methods ), showing no difference compared with ketamine/xylazine used for all other thresholds. Mean thresholds for mutants aged 2 weeks (yellow), 4 weeks (purple), 14 weeks (cyan), 28 weeks (grey) and 44 weeks (black). Averaged click‐evoked ABR waveforms from 4‐week‐old wt ( n = 23, green) and mutants ( n = 34, red), at 50‐ dB sensation level ( SL ) (left panel). SP and ABR wave 1 (W1) are indicated by grey areas. Expanded averaged SP and ABR W1 waveform patterns for 10‐ to 60‐ dB SL in 10‐ dB increments are plotted in green (wt; middle panel) and red (mutants; right panel), to illustrate the growth of SP and W1 with stimulus level. Mean 2f1‐f2 DPOAE thresholds (± SD ) are plotted for wt (green), heterozygote (blue) and homozygous (red) mice aged 4 weeks (H: wt, n = 5; hom, n = 5) or 21 weeks (I: het, n = 3; hom, n = 5), as a function of f2 frequency.

    Techniques Used: Mouse Assay

    Normal appearance of hair cell bundles and normal pre‐synaptic function in Wbp2‐deficient mice SEM showing normal appearance of IHC and OHC hair bundles in 6‐week‐old Wbp2‐deficient mice compared to wt controls, illustrated for the 24‐ kH z (40% of the length of the cochlear duct from the base) and 9‐ kH z (80% position) best frequency regions. There was no sign of excess degeneration up to 30 weeks in mutants compared to littermate controls. Scale bars: upper row, 20 μm; middle row, 3 μm; bottom row, 1 μm. Saturating mechanoelectrical transducer ( MET ) currents recorded from a P7 control and a Wbp2 ‐mutant IHC by applying voltage steps from −121 mV to +99 mV in 20‐ mV increments (holding potential −81 mV ). For clarity, only two voltage steps are shown. During the voltage steps, hair bundles were displaced by applying 50‐Hz sinusoidal force stimuli (the driver voltage, DV , to the fluid jet is shown above the traces). Negative deflections of the DV are inhibitory. The arrows indicate the closure of the transducer channels, that is disappearance of the resting current, during inhibitory bundle displacements. Dashed lines indicate the holding current, which is the current at the holding potential of −81 mV . Peak‐to‐peak current–voltage curves obtained from 11 controls and 5 Wbp2 ‐mutant IHC s (P7–P8). I C a and Δ C m responses from adult (P19–P33) control and Wbp2 ‐mutant IHC s from high‐frequency region. Recordings were obtained in response to 50‐ms voltage steps, in 10‐ mV increments, from −81 mV. For clarity, only average maximal responses are shown (control: n = 7; Wbp2 mutant: n = 8). Average peak I C a ‐voltage (left axis) and Δ C m ‐voltage (right axis) curves from control and Wbp2 ‐mutant IHC s (control: n = 7; Wbp2 mutant: n = 8). Average Δ C m from 10 control and 11 Wbp2 ‐mutant IHC s in response to voltage steps from 2 ms to 100 ms (to around −11 mV ) showing mainly the RRP and the initial recruitment of the SRP for the 100‐ms step. Average Δ C m from 12 control and 11 Wbp2 ‐mutant IHC s in response to voltage steps from 100 ms to 2 s (to around −11 mV ) showing the SRP . Data information: Data are shown as mean ± SD.
    Figure Legend Snippet: Normal appearance of hair cell bundles and normal pre‐synaptic function in Wbp2‐deficient mice SEM showing normal appearance of IHC and OHC hair bundles in 6‐week‐old Wbp2‐deficient mice compared to wt controls, illustrated for the 24‐ kH z (40% of the length of the cochlear duct from the base) and 9‐ kH z (80% position) best frequency regions. There was no sign of excess degeneration up to 30 weeks in mutants compared to littermate controls. Scale bars: upper row, 20 μm; middle row, 3 μm; bottom row, 1 μm. Saturating mechanoelectrical transducer ( MET ) currents recorded from a P7 control and a Wbp2 ‐mutant IHC by applying voltage steps from −121 mV to +99 mV in 20‐ mV increments (holding potential −81 mV ). For clarity, only two voltage steps are shown. During the voltage steps, hair bundles were displaced by applying 50‐Hz sinusoidal force stimuli (the driver voltage, DV , to the fluid jet is shown above the traces). Negative deflections of the DV are inhibitory. The arrows indicate the closure of the transducer channels, that is disappearance of the resting current, during inhibitory bundle displacements. Dashed lines indicate the holding current, which is the current at the holding potential of −81 mV . Peak‐to‐peak current–voltage curves obtained from 11 controls and 5 Wbp2 ‐mutant IHC s (P7–P8). I C a and Δ C m responses from adult (P19–P33) control and Wbp2 ‐mutant IHC s from high‐frequency region. Recordings were obtained in response to 50‐ms voltage steps, in 10‐ mV increments, from −81 mV. For clarity, only average maximal responses are shown (control: n = 7; Wbp2 mutant: n = 8). Average peak I C a ‐voltage (left axis) and Δ C m ‐voltage (right axis) curves from control and Wbp2 ‐mutant IHC s (control: n = 7; Wbp2 mutant: n = 8). Average Δ C m from 10 control and 11 Wbp2 ‐mutant IHC s in response to voltage steps from 2 ms to 100 ms (to around −11 mV ) showing mainly the RRP and the initial recruitment of the SRP for the 100‐ms step. Average Δ C m from 12 control and 11 Wbp2 ‐mutant IHC s in response to voltage steps from 100 ms to 2 s (to around −11 mV ) showing the SRP . Data information: Data are shown as mean ± SD.

    Techniques Used: Mouse Assay, Immunohistochemistry, Mutagenesis, Mass Spectrometry

    31) Product Images from "Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro – a potential pathway affecting proliferation"

    Article Title: Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro – a potential pathway affecting proliferation

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-20430-0

    Lung tissue expression of Cdkn1α in pulmonary fibrotic mice. Gene expression levels of Cdkn1α in lung tissue from control animals, BLM- and EXT5- and EXT9-treated mice were analyzed with rt-qPCR. The relative expressions of Cdkn1α , normalized to reference gene GAPDH , are presented as delta Ct values for each animal with group mean (n = 6). Statistical analysis was performed with one-way ANOVA.
    Figure Legend Snippet: Lung tissue expression of Cdkn1α in pulmonary fibrotic mice. Gene expression levels of Cdkn1α in lung tissue from control animals, BLM- and EXT5- and EXT9-treated mice were analyzed with rt-qPCR. The relative expressions of Cdkn1α , normalized to reference gene GAPDH , are presented as delta Ct values for each animal with group mean (n = 6). Statistical analysis was performed with one-way ANOVA.

    Techniques Used: Expressing, Mouse Assay, Quantitative RT-PCR

    32) Product Images from "Decreased TRPM7 inhibits activities and induces apoptosis of bladder cancer cells via ERK1/2 pathway"

    Article Title: Decreased TRPM7 inhibits activities and induces apoptosis of bladder cancer cells via ERK1/2 pathway

    Journal: Oncotarget

    doi: 10.18632/oncotarget.12146

    TRPM7 is upregulated in the BCa tissues and correlated with EMT markers ( A ) qRT-PCR analysis of relative gene expression of TRPM7 in total RNA isolated from ten BCa tissues at stage II, comparing with ten normal bladder tissues. Significance of TRPM7 expression difference was analyzed using T-test . * p
    Figure Legend Snippet: TRPM7 is upregulated in the BCa tissues and correlated with EMT markers ( A ) qRT-PCR analysis of relative gene expression of TRPM7 in total RNA isolated from ten BCa tissues at stage II, comparing with ten normal bladder tissues. Significance of TRPM7 expression difference was analyzed using T-test . * p

    Techniques Used: BIA-KA, Quantitative RT-PCR, Expressing, Isolation

    33) Product Images from "Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer"

    Article Title: Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer

    Journal: Oncotarget

    doi: 10.18632/oncotarget.24764

    Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p
    Figure Legend Snippet: Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p

    Techniques Used: Expressing, Software, Western Blot, Real-time Polymerase Chain Reaction

    34) Product Images from "Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines"

    Article Title: Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines

    Journal: BMC Research Notes

    doi: 10.1186/s13104-017-2959-0

    Primer location and RNA isolation method affect qPCR knockdown detection. qPCR was conducted on cDNA synthesized from total RNA samples and mRNA samples. Two primer sets—one amplifying 5′ of the siRNA cut site, the other amplifying 3′ of the siRNA cut site—were compared. Relative gene expression of a snr1 , b brm , c osa and d trr was measured by qPCR in third instar larvae after ubiquitous expression of UAS - RNAi constructs with Act - Gal4 . Expression levels were normalized to the reference genes, eIF2Bγ and βCOP . Shown here, are relative expression values compared to the UAS - mCherry - RNAi control (indicated by the dotted line). Asterisks directly above bars indicate a significant knockdown compared to the control, while asterisks above brackets indicate significant differences in gene expression between different conditions—total RNA vs. mRNA, 3′ vs. 5′ primer set (*p
    Figure Legend Snippet: Primer location and RNA isolation method affect qPCR knockdown detection. qPCR was conducted on cDNA synthesized from total RNA samples and mRNA samples. Two primer sets—one amplifying 5′ of the siRNA cut site, the other amplifying 3′ of the siRNA cut site—were compared. Relative gene expression of a snr1 , b brm , c osa and d trr was measured by qPCR in third instar larvae after ubiquitous expression of UAS - RNAi constructs with Act - Gal4 . Expression levels were normalized to the reference genes, eIF2Bγ and βCOP . Shown here, are relative expression values compared to the UAS - mCherry - RNAi control (indicated by the dotted line). Asterisks directly above bars indicate a significant knockdown compared to the control, while asterisks above brackets indicate significant differences in gene expression between different conditions—total RNA vs. mRNA, 3′ vs. 5′ primer set (*p

    Techniques Used: Isolation, Real-time Polymerase Chain Reaction, Synthesized, Expressing, Construct, Activated Clotting Time Assay

    Schematic representation of the experimental setup. siRNAs direct site-specific cleavage of mRNAs, resulting in a 5′ and 3′ mRNA cleavage fragments. After RNA isolation total RNA samples consist of uncleaved mRNA transcripts and non-coding RNA, as well as undegraded 5′ and 3′ mRNA cleavage fragments. Purification of mRNA using poly-T beads excludes 5′ mRNA cleavage fragments and non-coding RNAs that are not polyadenylated. As indicated by the boxes, 5′ and 3′ primer sets could detect different species of RNA depending on the isolation method
    Figure Legend Snippet: Schematic representation of the experimental setup. siRNAs direct site-specific cleavage of mRNAs, resulting in a 5′ and 3′ mRNA cleavage fragments. After RNA isolation total RNA samples consist of uncleaved mRNA transcripts and non-coding RNA, as well as undegraded 5′ and 3′ mRNA cleavage fragments. Purification of mRNA using poly-T beads excludes 5′ mRNA cleavage fragments and non-coding RNAs that are not polyadenylated. As indicated by the boxes, 5′ and 3′ primer sets could detect different species of RNA depending on the isolation method

    Techniques Used: Isolation, Purification

    35) Product Images from "Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications"

    Article Title: Simultaneous isolation of high-quality DNA, RNA, miRNA and proteins from tissues for genomic applications

    Journal: Nature protocols

    doi: 10.1038/nprot.2013.141

    Examples for DNA and RNA quality, and integrity from isolated samples. ( a ) Agarose gel electrophoresis of genomic DNA to verify that there is no DNA degradation resulting in a DNA ladder. ( b ) Representative electropherograms run with Bio-Rad Experion of RNA samples isolated as total RNA, high-molecular-weight RNA (enriched for mRNA) and low-molecular-weight RNA (enriched for ncRNA like miRNA). ( c ) Representative electropherogram for a good-quality RNA. ( d ) Representative electropherogram for a highly-degraded RNA. Abundant human ribosomal RNAs of 5S, 18S, and 28S are indicated.
    Figure Legend Snippet: Examples for DNA and RNA quality, and integrity from isolated samples. ( a ) Agarose gel electrophoresis of genomic DNA to verify that there is no DNA degradation resulting in a DNA ladder. ( b ) Representative electropherograms run with Bio-Rad Experion of RNA samples isolated as total RNA, high-molecular-weight RNA (enriched for mRNA) and low-molecular-weight RNA (enriched for ncRNA like miRNA). ( c ) Representative electropherogram for a good-quality RNA. ( d ) Representative electropherogram for a highly-degraded RNA. Abundant human ribosomal RNAs of 5S, 18S, and 28S are indicated.

    Techniques Used: Isolation, Agarose Gel Electrophoresis, Molecular Weight

    36) Product Images from "Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line"

    Article Title: Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line

    Journal: Biomedical Journal

    doi: 10.1016/j.bj.2018.05.002

    The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.
    Figure Legend Snippet: The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.

    Techniques Used: Expressing, Activation Assay

    Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.
    Figure Legend Snippet: Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.

    Techniques Used: Expressing, Polymerase Chain Reaction

    Estimation of cytochrome C levels in untreated and treated MCF-7 cells. Cells treated with laser alone or MPDC alone did not lead to an increased colorometric signal when compared to the untreated cells. PDT-treated cells showed a significant increase shown as *** ( p = 0.0005) and evidence of undergoing cell damage.
    Figure Legend Snippet: Estimation of cytochrome C levels in untreated and treated MCF-7 cells. Cells treated with laser alone or MPDC alone did not lead to an increased colorometric signal when compared to the untreated cells. PDT-treated cells showed a significant increase shown as *** ( p = 0.0005) and evidence of undergoing cell damage.

    Techniques Used:

    Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).
    Figure Legend Snippet: Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).

    Techniques Used: Irradiation

    37) Product Images from "Detailed characterization of tumor infiltrating lymphocytes in two distinct human solid malignancies show phenotypic similarities"

    Article Title: Detailed characterization of tumor infiltrating lymphocytes in two distinct human solid malignancies show phenotypic similarities

    Journal: Journal for Immunotherapy of Cancer

    doi: 10.1186/s40425-014-0038-9

    HLA-DR + TIL Treg have a higher suppressive potency. CD3 + CD4 + CD25 high and CD127 low Treg were sorted for HLA-DR+/−. Their suppressive function was measured in vitro by their capacity to suppress INFγ secretion by effector CD4 + T cells. Panel A and B represent 2 individual OVC patients.
    Figure Legend Snippet: HLA-DR + TIL Treg have a higher suppressive potency. CD3 + CD4 + CD25 high and CD127 low Treg were sorted for HLA-DR+/−. Their suppressive function was measured in vitro by their capacity to suppress INFγ secretion by effector CD4 + T cells. Panel A and B represent 2 individual OVC patients.

    Techniques Used: In Vitro

    HLA-DR expression on Treg and non-Treg CD4 + T cells. CD3 + CD4 + CD25 + FoxP3 + Treg cells were analyzed for HLA-DR expression in CRC samples (A) and OVC samples (B) . C . HLA-DR expression on CD4 + Foxp3 − non-Treg in OVC samples.
    Figure Legend Snippet: HLA-DR expression on Treg and non-Treg CD4 + T cells. CD3 + CD4 + CD25 + FoxP3 + Treg cells were analyzed for HLA-DR expression in CRC samples (A) and OVC samples (B) . C . HLA-DR expression on CD4 + Foxp3 − non-Treg in OVC samples.

    Techniques Used: Expressing

    Expression of markers characterizing more suppressive Treg. Panel A shows the expression of Helios CD39 and CTLA-4 on CD4 + CD25 + Foxp3 + Treg from an OVC sample. B . Expression of Helios on Treg cells. C . Co-expression of Helios and HLA-DR on Treg (OVC n = 17). D . Percentage of CD39 + Treg, E . Percentage of CD39-HLA-DR Treg (OVC n = 11). F . CTLA-4 expression and G . CD39-CTLA-4 expression on Treg from OVC samples (n = 10).
    Figure Legend Snippet: Expression of markers characterizing more suppressive Treg. Panel A shows the expression of Helios CD39 and CTLA-4 on CD4 + CD25 + Foxp3 + Treg from an OVC sample. B . Expression of Helios on Treg cells. C . Co-expression of Helios and HLA-DR on Treg (OVC n = 17). D . Percentage of CD39 + Treg, E . Percentage of CD39-HLA-DR Treg (OVC n = 11). F . CTLA-4 expression and G . CD39-CTLA-4 expression on Treg from OVC samples (n = 10).

    Techniques Used: Expressing

    CD4 + T cell analysis. A . CD3 + CD4 + T cells collected from PBL, ascites, primary tumor and omental metastases were analyzed for CD25 and FoxP3, upper panels and Ki-67 and Foxp3, lower panels. Percentage of CD25 + FoxP3 + , Treg in PBL and TIL of CRC patients (n = 16) B , and in OVC patients (n = 22) C . Percentage of proliferating Treg in CRC samples (D) and in OVC samples (E) .
    Figure Legend Snippet: CD4 + T cell analysis. A . CD3 + CD4 + T cells collected from PBL, ascites, primary tumor and omental metastases were analyzed for CD25 and FoxP3, upper panels and Ki-67 and Foxp3, lower panels. Percentage of CD25 + FoxP3 + , Treg in PBL and TIL of CRC patients (n = 16) B , and in OVC patients (n = 22) C . Percentage of proliferating Treg in CRC samples (D) and in OVC samples (E) .

    Techniques Used:

    Expression of IL-6 by qPCR in PBL and TIL. CD4 + T cells were enriched from paired blood and tumor specimens and qPCR was performed on the enriched cell populations as described in Methods . The fold difference in IL-6 message in the TIL was normalized to the paired PBL in CRC samples (A) and OC samples (B) .
    Figure Legend Snippet: Expression of IL-6 by qPCR in PBL and TIL. CD4 + T cells were enriched from paired blood and tumor specimens and qPCR was performed on the enriched cell populations as described in Methods . The fold difference in IL-6 message in the TIL was normalized to the paired PBL in CRC samples (A) and OC samples (B) .

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction

    38) Product Images from "Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines"

    Article Title: Optimal RNA isolation method and primer design to detect gene knockdown by qPCR when validating Drosophila transgenic RNAi lines

    Journal: BMC Research Notes

    doi: 10.1186/s13104-017-2959-0

    Primer location and RNA isolation method affect qPCR knockdown detection. qPCR was conducted on cDNA synthesized from total RNA samples and mRNA samples. Two primer sets—one amplifying 5′ of the siRNA cut site, the other amplifying 3′ of the siRNA cut site—were compared. Relative gene expression of a snr1 , b brm , c osa and d trr was measured by qPCR in third instar larvae after ubiquitous expression of UAS - RNAi constructs with Act - Gal4 . Expression levels were normalized to the reference genes, eIF2Bγ and βCOP . Shown here, are relative expression values compared to the UAS - mCherry - RNAi control (indicated by the dotted line). Asterisks directly above bars indicate a significant knockdown compared to the control, while asterisks above brackets indicate significant differences in gene expression between different conditions—total RNA vs. mRNA, 3′ vs. 5′ primer set (*p
    Figure Legend Snippet: Primer location and RNA isolation method affect qPCR knockdown detection. qPCR was conducted on cDNA synthesized from total RNA samples and mRNA samples. Two primer sets—one amplifying 5′ of the siRNA cut site, the other amplifying 3′ of the siRNA cut site—were compared. Relative gene expression of a snr1 , b brm , c osa and d trr was measured by qPCR in third instar larvae after ubiquitous expression of UAS - RNAi constructs with Act - Gal4 . Expression levels were normalized to the reference genes, eIF2Bγ and βCOP . Shown here, are relative expression values compared to the UAS - mCherry - RNAi control (indicated by the dotted line). Asterisks directly above bars indicate a significant knockdown compared to the control, while asterisks above brackets indicate significant differences in gene expression between different conditions—total RNA vs. mRNA, 3′ vs. 5′ primer set (*p

    Techniques Used: Isolation, Real-time Polymerase Chain Reaction, Synthesized, Expressing, Construct, Activated Clotting Time Assay

    39) Product Images from "Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro – a potential pathway affecting proliferation"

    Article Title: Pulmonary fibrosis in vivo displays increased p21 expression reduced by 5-HT2B receptor antagonists in vitro – a potential pathway affecting proliferation

    Journal: Scientific Reports

    doi: 10.1038/s41598-018-20430-0

    Lung tissue expression of Cdkn1α in pulmonary fibrotic mice. Gene expression levels of Cdkn1α in lung tissue from control animals, BLM- and EXT5- and EXT9-treated mice were analyzed with rt-qPCR. The relative expressions of Cdkn1α , normalized to reference gene GAPDH , are presented as delta Ct values for each animal with group mean (n = 6). Statistical analysis was performed with one-way ANOVA.
    Figure Legend Snippet: Lung tissue expression of Cdkn1α in pulmonary fibrotic mice. Gene expression levels of Cdkn1α in lung tissue from control animals, BLM- and EXT5- and EXT9-treated mice were analyzed with rt-qPCR. The relative expressions of Cdkn1α , normalized to reference gene GAPDH , are presented as delta Ct values for each animal with group mean (n = 6). Statistical analysis was performed with one-way ANOVA.

    Techniques Used: Expressing, Mouse Assay, Quantitative RT-PCR

    Venn diagram of statistically significant differentially expressed genes in BLM-, EXT5 and EXT9-treated mice. Distal lung tissue from mice subjected to s.c. administrations of BLM in combination with p.o. treatment with EXT5, EXT9 or saline was isolated for RNA. With whole genome gene expression array and SAM analysis, significant differentially expressed genes were identified, in comparison to healthy saline controls. p
    Figure Legend Snippet: Venn diagram of statistically significant differentially expressed genes in BLM-, EXT5 and EXT9-treated mice. Distal lung tissue from mice subjected to s.c. administrations of BLM in combination with p.o. treatment with EXT5, EXT9 or saline was isolated for RNA. With whole genome gene expression array and SAM analysis, significant differentially expressed genes were identified, in comparison to healthy saline controls. p

    Techniques Used: Mouse Assay, Isolation, Expressing

    40) Product Images from "Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer"

    Article Title: Synthesis and anticancer activity of the derivatives of marine compound rhizochalin in castration resistant prostate cancer

    Journal: Oncotarget

    doi: 10.18632/oncotarget.24764

    Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p
    Figure Legend Snippet: Effect of rhizochalinin (2) and 18-hydroxyrhizochalinin (4) on the expression of different genes, controlled by AR-FL and AR-V7 ( A ) Analysis of AR-V7 and AR-FL protein expression in different human prostate cancer cells lines. ( B , C ) mRNA expression levels of the genes controlled by AR-V7 (B) or AR-FL (C). 22Rv1 cells were pre-treated with the indicated concentrations of investigated compounds in 0.1% FBS/RPMI media for 30 min followed by co-treatment with 20 nM DHT for another 24 h. ( D ) Analysis of AR-V7 expression in 22Rv1 cells lines treated with compounds (2) and (4) for 48 h. Signal intensity was quantified with Quantity One 4.6 software and normalized to the signal of α-tubulin. Protein expression was analyzed by Western blotting. mRNA expression was analysed by qPCR. * p

    Techniques Used: Expressing, Software, Western Blot, Real-time Polymerase Chain Reaction

    41) Product Images from "Decreased TRPM7 inhibits activities and induces apoptosis of bladder cancer cells via ERK1/2 pathway"

    Article Title: Decreased TRPM7 inhibits activities and induces apoptosis of bladder cancer cells via ERK1/2 pathway

    Journal: Oncotarget

    doi: 10.18632/oncotarget.12146

    TRPM7 is upregulated in the BCa tissues and correlated with EMT markers ( A ) qRT-PCR analysis of relative gene expression of TRPM7 in total RNA isolated from ten BCa tissues at stage II, comparing with ten normal bladder tissues. Significance of TRPM7 expression difference was analyzed using T-test . * p
    Figure Legend Snippet: TRPM7 is upregulated in the BCa tissues and correlated with EMT markers ( A ) qRT-PCR analysis of relative gene expression of TRPM7 in total RNA isolated from ten BCa tissues at stage II, comparing with ten normal bladder tissues. Significance of TRPM7 expression difference was analyzed using T-test . * p

    Techniques Used: BIA-KA, Quantitative RT-PCR, Expressing, Isolation

    42) Product Images from "Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line"

    Article Title: Evaluation of cell damage induced by irradiated Zinc-Phthalocyanine-gold dendrimeric nanoparticles in a breast cancer cell line

    Journal: Biomedical Journal

    doi: 10.1016/j.bj.2018.05.002

    The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.
    Figure Legend Snippet: The primary response of MPDC-mediated PDT on the expression of genes involved in cell death pathways was the up-regulation of Ulk-1, Bax, Casp-2 and Bcl-2 genes. The Ulk-1 protein protonates and activates the FIP200. ULK is part of a protein complex containing Atg13, Atg17 and FIP200 (autophagosome), which drives the subsequent cellular damage and death. The Bax protein directly affects the mitochondria while the Cas-2 protein is activated by reactive oxygen species (ROS) and then Casp-2 transforms a mitochondrial damaging protein into its truncated and activated form (tBid). The p53-induced death domain associated protein (PIDD) can also convert pro-Casp-2 into the active Casp-2. Apoptogenic proteins (such as Cytochrome C) released from mitochondria participate in the assemblage of the apoptosome, activation of other effectors (Casp-3/6/7) and cell death. Mitochondrial damage and depolarization induce change in cellular ATP levels, activation of the 5′ adenosine monophosphate activated protein kinase (AMPK) and AMPK-induced cell death. This cell death response stimulates Bcl-2 protein to prevent further cell damage.

    Techniques Used: Expressing, Activation Assay

    Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.
    Figure Legend Snippet: Gene expression profiles of PDT-treated MCF-7 cells with 0.3 μM MPDC and 10 J/cm 2 was analyzed using the SABiosciences Human Cell Death Pathway Finder Profiler™ PCR Array System. PDT-induced changes in gene expression and BAX, BCL-2, CASP-2 and ULK-1 genes were significantly up-regulated as represented in the volcano plot. In the volcano plot, the horizontal line designates the target threshold ( p = 0.05) and vertical lines, the fold change (central) and target fold change threshold (peripheral) in gene expression.

    Techniques Used: Expressing, Polymerase Chain Reaction

    Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).
    Figure Legend Snippet: Morphology of untreated, irradiated, MPDC-treated and PDT-treated MCF-7 cells. No morphological change was noted in irradiated or MPDC treated cells when compared to untreated cells. The morphology of PDT-treated MCF-7 cells changed, include an elongation of cells, decrease in cell number, detachment and rounding off (200× magnification).

    Techniques Used: Irradiation

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    Centrifugation:

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    Amplification:

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    Real-time Polymerase Chain Reaction:

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    Microarray:

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    Incubation:

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    Expressing:

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    Modification:

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    Flow Cytometry:

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    Polymerase Chain Reaction:

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    Binding Assay:

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    DNA Extraction:

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    Reverse Transcription Polymerase Chain Reaction:

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    Purification:

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    RNA Extraction:

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    Selection:

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    Agarose Gel Electrophoresis:

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    Homogenization:

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    Spectrophotometry:

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    Concentration Assay:

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    Lysis:

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    Gradient Centrifugation:

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    View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and <t>QIAshredder-pellet</t> was performed to derive each Ct value. The numbers in each graph are Ct values.
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    View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.

    Journal: PLoS ONE

    Article Title: Convenient Detection of the Citrus Greening (Huanglongbing) Bacterium 'Candidatus Liberibacter asiaticus' by Direct PCR from the Midrib Extract

    doi: 10.1371/journal.pone.0057011

    Figure Lengend Snippet: View of threshold (Ct) values derived from real-time PCR. Ct values were compared among PCR amplifications using three preparation methods and two primer sets. In each of 11 Las-infected citrus leaf samples, real-time PCR using Las606/LSS and OI1/OI2c primer sets with templates obtained from Extracted DNA , Biomasher-pellet , and QIAshredder-pellet was performed to derive each Ct value. The numbers in each graph are Ct values.

    Article Snippet: However, when the preparation using QIAshredder spin column will be modified, the sensitivity of detection may be improved.

    Techniques: Derivative Assay, Real-time Polymerase Chain Reaction, Polymerase Chain Reaction, Infection

    Study concept . (A) Total RNA of each of the first 24 samples had been extracted following three different total RNA purification methods A, B, and C. Method A: lysis of the mononuclear cells, followed by lysate homogenization (to reduce viscosity caused by high-molecular-weight cellular components and cell debris) using a biopolymer shredding system in a microcentrifuge spin-column format (QIAshredder, Qiagen) followed by total RNA purification (RNeasy Mini Kit, Qiagen). Method B: TRIzol RNA isolation (Invitrogen). Method C: TRIzol RNA isolation (Invitrogen) followed by an RNeasy purification step (RNeasy Mini Kit, Qiagen). The RNA purification step combines the selective binding properties of a silica-based membrane with the speed of microspin technology. It allows only RNA longer than 200 bases to bind to the silica membrane, providing an enriching for mRNA since nucleotides shorter than 200 nucleotides are selectively excluded. (B) For each of three additional samples, nine aliquots of mononuclear cells had been collected. Total RNA has been processed for each aliquot following one of the three methods and for each method three independent technical replicates were performed (A,A,A, B,B,B, C,C,C).

    Journal: BMC Genomics

    Article Title: New data on robustness of gene expression signatures in leukemia: comparison of three distinct total RNA preparation procedures

    doi: 10.1186/1471-2164-8-188

    Figure Lengend Snippet: Study concept . (A) Total RNA of each of the first 24 samples had been extracted following three different total RNA purification methods A, B, and C. Method A: lysis of the mononuclear cells, followed by lysate homogenization (to reduce viscosity caused by high-molecular-weight cellular components and cell debris) using a biopolymer shredding system in a microcentrifuge spin-column format (QIAshredder, Qiagen) followed by total RNA purification (RNeasy Mini Kit, Qiagen). Method B: TRIzol RNA isolation (Invitrogen). Method C: TRIzol RNA isolation (Invitrogen) followed by an RNeasy purification step (RNeasy Mini Kit, Qiagen). The RNA purification step combines the selective binding properties of a silica-based membrane with the speed of microspin technology. It allows only RNA longer than 200 bases to bind to the silica membrane, providing an enriching for mRNA since nucleotides shorter than 200 nucleotides are selectively excluded. (B) For each of three additional samples, nine aliquots of mononuclear cells had been collected. Total RNA has been processed for each aliquot following one of the three methods and for each method three independent technical replicates were performed (A,A,A, B,B,B, C,C,C).

    Article Snippet: Method A: lysis of the mononuclear cells, followed by lysate homogenization using a biopolymer shredding system in a microcentrifuge spin-column format (QIAshredder, Qiagen, Hilden, Germany), followed by total RNA purification using selective binding columns (RNeasy Mini Kit, Qiagen).

    Techniques: Purification, Lysis, Homogenization, Molecular Weight, Isolation, Binding Assay

    Analysis of technical bias to perceived community composition. (A) NMDS of the 16S rRNA gene amplicon sequencing data based on a Bray-Curtis dissimilarity matrix generated after random subsampling of 2,800 sequences from each sample. Bars indicate the range of coordinates for the three replicate extractions/sequencing datasets per treatment. (B) Phylum level data (top 10 most abundant phyla, fractions of all reads). Number 1–3 between parentheses indicates the sequencing run from which each dataset is derived. APO combines three slightly different treatments that did not result in significantly different taxonomic representations ( S2 Fig .). Acronyms: Extraction protocols: APS (standard AllPrep protocol), APO (optimized AllPrep protocol), Enz (Enzymatic protocol), Bead (Bead-beating protocol); Preservation methods: NT (none), RL (RNAlater), RP (RNAprotect), BU (Qiagen Lysis Buffer RLT+); Other modifications: LYS (lysozyme), NQ (No QIAshredder column), TL (bead-beating with TissueLyser). Except for the APO samples, none of the Douglas Lake filters were preserved in RNA protection agents.

    Journal: PLoS ONE

    Article Title: RNA Preservation Agents and Nucleic Acid Extraction Method Bias Perceived Bacterial Community Composition

    doi: 10.1371/journal.pone.0121659

    Figure Lengend Snippet: Analysis of technical bias to perceived community composition. (A) NMDS of the 16S rRNA gene amplicon sequencing data based on a Bray-Curtis dissimilarity matrix generated after random subsampling of 2,800 sequences from each sample. Bars indicate the range of coordinates for the three replicate extractions/sequencing datasets per treatment. (B) Phylum level data (top 10 most abundant phyla, fractions of all reads). Number 1–3 between parentheses indicates the sequencing run from which each dataset is derived. APO combines three slightly different treatments that did not result in significantly different taxonomic representations ( S2 Fig .). Acronyms: Extraction protocols: APS (standard AllPrep protocol), APO (optimized AllPrep protocol), Enz (Enzymatic protocol), Bead (Bead-beating protocol); Preservation methods: NT (none), RL (RNAlater), RP (RNAprotect), BU (Qiagen Lysis Buffer RLT+); Other modifications: LYS (lysozyme), NQ (No QIAshredder column), TL (bead-beating with TissueLyser). Except for the APO samples, none of the Douglas Lake filters were preserved in RNA protection agents.

    Article Snippet: The lysate was transferred to a QIAshredder column (Qiagen) and the remainder of the protocol was performed according to the manufacturer’s instructions, performing two elution steps with of 30 μl elution buffer for both RNA and DNA.

    Techniques: Amplification, Sequencing, Generated, Derivative Assay, Preserving, Lysis