rna  (Roche)


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    Structured Review

    Roche rna
    ( A ) Pedigree. In this family, the proband (arrowed) inherited a synonymous PKD1 variant (c.2097G > T, p. Ser699=) from his mother. ( B ) RT-PCR from whole blood <t>RNA.</t> In the control sample (Wt), only the expected 585 bp fragment was present. In the patient sample (P), an additional 1038 bp abnormal fragment was amplified. ( C ) Sequencing of the regular and abnormal fragments from the patient sample. In the upper panel, the sequence of the 585 bp normal c.2097G allele <t>cDNA</t> showing the adjacent exons 10 and 11, correctly spliced; in the lower panel, the sequence of the abnormal 1038 bp cDNA showing that in the mutated allele c.2097T, intron 10 has been completely retained in the transcript. ( D ) A scheme of the spliced regions in the normal and mutant alleles. Filled symbol: ADPKD; empty symbol: healthy subject.
    Rna, supplied by Roche, used in various techniques. Bioz Stars score: 93/100, based on 5251 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Images

    1) Product Images from "Deciphering Variability of PKD1 and PKD2 in an Italian Cohort of 643 Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD)"

    Article Title: Deciphering Variability of PKD1 and PKD2 in an Italian Cohort of 643 Patients with Autosomal Dominant Polycystic Kidney Disease (ADPKD)

    Journal: Scientific Reports

    doi: 10.1038/srep30850

    ( A ) Pedigree. In this family, the proband (arrowed) inherited a synonymous PKD1 variant (c.2097G > T, p. Ser699=) from his mother. ( B ) RT-PCR from whole blood RNA. In the control sample (Wt), only the expected 585 bp fragment was present. In the patient sample (P), an additional 1038 bp abnormal fragment was amplified. ( C ) Sequencing of the regular and abnormal fragments from the patient sample. In the upper panel, the sequence of the 585 bp normal c.2097G allele cDNA showing the adjacent exons 10 and 11, correctly spliced; in the lower panel, the sequence of the abnormal 1038 bp cDNA showing that in the mutated allele c.2097T, intron 10 has been completely retained in the transcript. ( D ) A scheme of the spliced regions in the normal and mutant alleles. Filled symbol: ADPKD; empty symbol: healthy subject.
    Figure Legend Snippet: ( A ) Pedigree. In this family, the proband (arrowed) inherited a synonymous PKD1 variant (c.2097G > T, p. Ser699=) from his mother. ( B ) RT-PCR from whole blood RNA. In the control sample (Wt), only the expected 585 bp fragment was present. In the patient sample (P), an additional 1038 bp abnormal fragment was amplified. ( C ) Sequencing of the regular and abnormal fragments from the patient sample. In the upper panel, the sequence of the 585 bp normal c.2097G allele cDNA showing the adjacent exons 10 and 11, correctly spliced; in the lower panel, the sequence of the abnormal 1038 bp cDNA showing that in the mutated allele c.2097T, intron 10 has been completely retained in the transcript. ( D ) A scheme of the spliced regions in the normal and mutant alleles. Filled symbol: ADPKD; empty symbol: healthy subject.

    Techniques Used: Variant Assay, Reverse Transcription Polymerase Chain Reaction, Amplification, Sequencing, Mutagenesis

    2) Product Images from "A set of isomeric episomal plasmids for systematic examination of mitotic stability in Saccharomyces cerevisiae) A set of isomeric episomal plasmids for systematic examination of mitotic stability in Saccharomyces cerevisiae"

    Article Title: A set of isomeric episomal plasmids for systematic examination of mitotic stability in Saccharomyces cerevisiae) A set of isomeric episomal plasmids for systematic examination of mitotic stability in Saccharomyces cerevisiae

    Journal: Yeast (Chichester, England)

    doi: 10.1002/yea.3231

    Isomeric forms of a basic E. coli ‐yeast shuttle vector carrying a yeast HIS3 marker gene. (a) (Open arrow) Bacterial fragment [1924 bp , amplified from pUG34 (GenBank: AF298784.1)] with oriV and bla , where the arrow marks the direction of transcription of the bla gene. (Shaded arrow) yeast 2 μm fragment [1405 bp (GenBank: J01347.1), amplified from the native 2 μm (B form) of Saccharomyces cerevisiae strain SY992 (Tomlin et al. , 2001 )] with terminator sequences of the REP3 gene, STB , ori , an FRT sequence, and the 3′ region of the FLP gene (the 3′‐end of the FLP coding sequences as well as its terminator), where the arrow marks the direction of transcription of the FLP gene. (Black arrow) S. cerevisiae HIS3 gene (1017 bp , YOR202W, amplified from pUG34), where the arrow marks the direction of transcription of the HIS3 gene. Sa, Sac I; B1, Sna BI; Pv, Pvu I; Ss, Ssp I; Hp, Hpa I. (b) pIFC3.11, simplified drawing made with Snapgene Viewer. (c) pIFC plasmid family (schematic drawing); pIFC2.01–pIFC2.02 plasmids are 3329 bp long, pIFC3.11–pIFC3.24 are 4.346 bp .
    Figure Legend Snippet: Isomeric forms of a basic E. coli ‐yeast shuttle vector carrying a yeast HIS3 marker gene. (a) (Open arrow) Bacterial fragment [1924 bp , amplified from pUG34 (GenBank: AF298784.1)] with oriV and bla , where the arrow marks the direction of transcription of the bla gene. (Shaded arrow) yeast 2 μm fragment [1405 bp (GenBank: J01347.1), amplified from the native 2 μm (B form) of Saccharomyces cerevisiae strain SY992 (Tomlin et al. , 2001 )] with terminator sequences of the REP3 gene, STB , ori , an FRT sequence, and the 3′ region of the FLP gene (the 3′‐end of the FLP coding sequences as well as its terminator), where the arrow marks the direction of transcription of the FLP gene. (Black arrow) S. cerevisiae HIS3 gene (1017 bp , YOR202W, amplified from pUG34), where the arrow marks the direction of transcription of the HIS3 gene. Sa, Sac I; B1, Sna BI; Pv, Pvu I; Ss, Ssp I; Hp, Hpa I. (b) pIFC3.11, simplified drawing made with Snapgene Viewer. (c) pIFC plasmid family (schematic drawing); pIFC2.01–pIFC2.02 plasmids are 3329 bp long, pIFC3.11–pIFC3.24 are 4.346 bp .

    Techniques Used: Plasmid Preparation, Marker, Amplification, Sequencing

    3) Product Images from "Functional Analysis of the Exocyst Subunit Sec15 in Candida albicans"

    Article Title: Functional Analysis of the Exocyst Subunit Sec15 in Candida albicans

    Journal: Eukaryotic Cell

    doi: 10.1128/EC.00147-15

    Construction of C. albicans strain tetR-SEC15. (A) Southern blot analysis was performed on genomic DNA digested with restriction enzymes HindIII and EcoRV. A 1-kb DIG-labeled PCR amplicon was used as a probe that hybridizes to a region extending from 500 nt upstream of the SEC15 open reading frame and includes the first 500 nt of the open reading frame of SEC15 . Detection of fragments of the expected sizes for the wild-type allele in strain THE1 ( SEC15 ; 3.2 kb), URA3 -disrupted allele in strain SEC15 Δ/− ( sec15 Δ:: dpl200-URA3-dpl200 ; 0.8 kb), URA3 -loop-out allele in strain SEC15 FOA ( sec15 Δ:: dpl200 ; 1.1 kb), and tetO -regulated allele in strain tetR-SEC15 ( URA3-tetO-SEC15 ; 2.3 kb and 2.7 kb) is shown. (B) Transcriptional analyses of SEC15 were performed using mRNA extracted from strains THE1-CIp10 and tetR-SEC15 after growth for 2 h under nonrepressing (without DOX) and repressing (with DOX) conditions. mRNA was used as the template for reverse transcriptase PCR (RT-PCR) to amplify a 512-bp amplicon. There was no amplicon in strain tetR-SEC15 after growth with DOX for 2 h, in contrast to controls.
    Figure Legend Snippet: Construction of C. albicans strain tetR-SEC15. (A) Southern blot analysis was performed on genomic DNA digested with restriction enzymes HindIII and EcoRV. A 1-kb DIG-labeled PCR amplicon was used as a probe that hybridizes to a region extending from 500 nt upstream of the SEC15 open reading frame and includes the first 500 nt of the open reading frame of SEC15 . Detection of fragments of the expected sizes for the wild-type allele in strain THE1 ( SEC15 ; 3.2 kb), URA3 -disrupted allele in strain SEC15 Δ/− ( sec15 Δ:: dpl200-URA3-dpl200 ; 0.8 kb), URA3 -loop-out allele in strain SEC15 FOA ( sec15 Δ:: dpl200 ; 1.1 kb), and tetO -regulated allele in strain tetR-SEC15 ( URA3-tetO-SEC15 ; 2.3 kb and 2.7 kb) is shown. (B) Transcriptional analyses of SEC15 were performed using mRNA extracted from strains THE1-CIp10 and tetR-SEC15 after growth for 2 h under nonrepressing (without DOX) and repressing (with DOX) conditions. mRNA was used as the template for reverse transcriptase PCR (RT-PCR) to amplify a 512-bp amplicon. There was no amplicon in strain tetR-SEC15 after growth with DOX for 2 h, in contrast to controls.

    Techniques Used: Southern Blot, Labeling, Polymerase Chain Reaction, Amplification, Reverse Transcription Polymerase Chain Reaction

    4) Product Images from "Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies"

    Article Title: Amplicon-based semiconductor sequencing of human exomes: performance evaluation and optimization strategies

    Journal: Human Genetics

    doi: 10.1007/s00439-016-1656-8

    AmpliSeq exome properties and target region analysis. a Length density distribution calculated from the dimension of amplicons generated with the AmpliSeq Exome kit as determined from the provided BED. In the kit design, most of the CDS exons are covered by a single amplicon ( b ). The comparison of target regions across 6 different enrichment kits ( c ) revealed that no one fully address all the human CDS nor relevant clinical genes. The bar graph represents the number of genes with at least one exon partially addressed ( green ) or completely missed ( red ). Compared exome capture kits include: AmpliSeq Exome and TargetSeq Exome (Life Technologies), SureSelect Human All Exon v5/v6 (Agilent Technologies) and SeqCap EZ v2/v3 (Roche)
    Figure Legend Snippet: AmpliSeq exome properties and target region analysis. a Length density distribution calculated from the dimension of amplicons generated with the AmpliSeq Exome kit as determined from the provided BED. In the kit design, most of the CDS exons are covered by a single amplicon ( b ). The comparison of target regions across 6 different enrichment kits ( c ) revealed that no one fully address all the human CDS nor relevant clinical genes. The bar graph represents the number of genes with at least one exon partially addressed ( green ) or completely missed ( red ). Compared exome capture kits include: AmpliSeq Exome and TargetSeq Exome (Life Technologies), SureSelect Human All Exon v5/v6 (Agilent Technologies) and SeqCap EZ v2/v3 (Roche)

    Techniques Used: Generated, Amplification

    5) Product Images from "Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome"

    Article Title: Evaluation of Methods for the Extraction and Purification of DNA from the Human Microbiome

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0033865

    Boxplot of Euclidean distances between observed and grand proportions. To calculate grand proportions, the total counts of 16S rRNA gene reads of each species were calculated for eight replicates of each method. Then grand proportions were calculated based on total counts of 16S rRNA gene reads of each species per method. Grand proportions were used to calculate Euclidean distances between observed and grand proportions.
    Figure Legend Snippet: Boxplot of Euclidean distances between observed and grand proportions. To calculate grand proportions, the total counts of 16S rRNA gene reads of each species were calculated for eight replicates of each method. Then grand proportions were calculated based on total counts of 16S rRNA gene reads of each species per method. Grand proportions were used to calculate Euclidean distances between observed and grand proportions.

    Techniques Used:

    6) Product Images from "Cloning of the koi herpesvirus (KHV) gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis"

    Article Title: Cloning of the koi herpesvirus (KHV) gene encoding thymidine kinase and its use for a highly sensitive PCR based diagnosis

    Journal: BMC Microbiology

    doi: 10.1186/1471-2180-5-13

    Analysis of KHV TK mRNA in KF-1 cell line infected with KHV . KF-1 cells were infected with KHV. At 0 to 7 days post infection total mRNA was prepared from the infected cells and was used in an RT-PCR reaction using primers TK-Rtforward- TK and RTr long (A). 0 time control mRNA was prepared immediately after infection. lanes: M- size markers, 1–8- mRNA of days 0–7 post infection, 9- direct PCR of KHV DNA, 10- uninfected KF-1 cells 11- RNase treated mRNA of day 5 post infection. To confirm the identity of the RT-PCR products, Southern blot hybridization (B) was performed using the cloned TK gene as probe and mRNA of days 0–7 lanes 1–8 consecutively, control KHV – lane 9, and uninfected KF-1 cells as negative control – lane10. The arrow marks the position of the 621 bp product.
    Figure Legend Snippet: Analysis of KHV TK mRNA in KF-1 cell line infected with KHV . KF-1 cells were infected with KHV. At 0 to 7 days post infection total mRNA was prepared from the infected cells and was used in an RT-PCR reaction using primers TK-Rtforward- TK and RTr long (A). 0 time control mRNA was prepared immediately after infection. lanes: M- size markers, 1–8- mRNA of days 0–7 post infection, 9- direct PCR of KHV DNA, 10- uninfected KF-1 cells 11- RNase treated mRNA of day 5 post infection. To confirm the identity of the RT-PCR products, Southern blot hybridization (B) was performed using the cloned TK gene as probe and mRNA of days 0–7 lanes 1–8 consecutively, control KHV – lane 9, and uninfected KF-1 cells as negative control – lane10. The arrow marks the position of the 621 bp product.

    Techniques Used: Infection, Reverse Transcription Polymerase Chain Reaction, Polymerase Chain Reaction, Southern Blot, Hybridization, Clone Assay, Negative Control

    Sensitivity of three PCR assays for the diagnosis of KHV infection . A TK based PCR was used to detect KHV DNA and was compared to two other PCR protocols: the Gilad et al . (2002) and Gray et al . (2002). Details of primers, products and protocols are described in table 1. To compare the sensitivities of the assays, 10 fold serial dilutions of purified KHV DNA were prepared starting from 10 ng DNA per PCR reaction. PCR products were analyzed on a 1% agarose gel and visualized by ethidium bromide. For each protocol the highest dilutions that still give products are shown. The arrows denote the 200 and 500 bp. size markers.
    Figure Legend Snippet: Sensitivity of three PCR assays for the diagnosis of KHV infection . A TK based PCR was used to detect KHV DNA and was compared to two other PCR protocols: the Gilad et al . (2002) and Gray et al . (2002). Details of primers, products and protocols are described in table 1. To compare the sensitivities of the assays, 10 fold serial dilutions of purified KHV DNA were prepared starting from 10 ng DNA per PCR reaction. PCR products were analyzed on a 1% agarose gel and visualized by ethidium bromide. For each protocol the highest dilutions that still give products are shown. The arrows denote the 200 and 500 bp. size markers.

    Techniques Used: Polymerase Chain Reaction, Infection, Purification, Agarose Gel Electrophoresis

    7) Product Images from "Human papillomavirus in premalignant oral lesions: No evidence of association in a Spanish cohort"

    Article Title: Human papillomavirus in premalignant oral lesions: No evidence of association in a Spanish cohort

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0210070

    Pictures of HE and p16 INK4a IHC of 3 out 4 HPV-DNA positive cases. Patient 1. (10X) Severe dysplasia at HE stain, HPV16 positivity and 26–50% staining for p16. Patient 2. (10X) Oral lichen planus at HE stain, HPV 16 positivity and negative staining for p16. Patient 3. (10X) Moderate dysplasia at HE stain, HPV18 positivity and 26–50% staining for p16. HE: hematoxilyn and eosin stain.
    Figure Legend Snippet: Pictures of HE and p16 INK4a IHC of 3 out 4 HPV-DNA positive cases. Patient 1. (10X) Severe dysplasia at HE stain, HPV16 positivity and 26–50% staining for p16. Patient 2. (10X) Oral lichen planus at HE stain, HPV 16 positivity and negative staining for p16. Patient 3. (10X) Moderate dysplasia at HE stain, HPV18 positivity and 26–50% staining for p16. HE: hematoxilyn and eosin stain.

    Techniques Used: Immunohistochemistry, H&E Stain, Staining, Negative Staining

    8) Product Images from "Next generation sequencing and comparative analyses of Xenopus mitogenomes"

    Article Title: Next generation sequencing and comparative analyses of Xenopus mitogenomes

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-13-496

    Ratios of nonsynonymous/synonymous (dN/dS) nucleotide substitutions between the protein-coding genes of xenopus mitochondrial genomes. Although the ratios differ considerably between genes, complexes and pairs of species, in all cases genes are evolving under negative (purifying) selective pressure (dN/dS
    Figure Legend Snippet: Ratios of nonsynonymous/synonymous (dN/dS) nucleotide substitutions between the protein-coding genes of xenopus mitochondrial genomes. Although the ratios differ considerably between genes, complexes and pairs of species, in all cases genes are evolving under negative (purifying) selective pressure (dN/dS

    Techniques Used:

    Xenopus borealis mitochondrial genome. The complete mitochondrial genome of Xenopus borealis (17,474 bp, drawn to scale) All 13 protein coding genes are shown as open arrows, 2 ribosomal RNAs as shaded arrows and 22 tRNAs as arrowed lines. Each tRNA is shown by its single letter amino acid code. The two leucine and two serine tRNAs are differentiated by their respective anti-codons. The direction of transcription is indicated by the arrows. Also shown is the non-coding D-loop (control region, black) and the position of the primers (LongF1/R2 and LongF2/R1) used to generate the two long-PCR amplicons, which were pooled and sequenced using 454 technology.
    Figure Legend Snippet: Xenopus borealis mitochondrial genome. The complete mitochondrial genome of Xenopus borealis (17,474 bp, drawn to scale) All 13 protein coding genes are shown as open arrows, 2 ribosomal RNAs as shaded arrows and 22 tRNAs as arrowed lines. Each tRNA is shown by its single letter amino acid code. The two leucine and two serine tRNAs are differentiated by their respective anti-codons. The direction of transcription is indicated by the arrows. Also shown is the non-coding D-loop (control region, black) and the position of the primers (LongF1/R2 and LongF2/R1) used to generate the two long-PCR amplicons, which were pooled and sequenced using 454 technology.

    Techniques Used: Polymerase Chain Reaction

    Phylogenetic estimates of the interrelationship of four xenopus species and two relatives based on Bayesian analysis of amino acids from concatenated protein coding sequences. Nodal support is given by posterior probabilities; branch-length scale indicates number of substitutions per site.
    Figure Legend Snippet: Phylogenetic estimates of the interrelationship of four xenopus species and two relatives based on Bayesian analysis of amino acids from concatenated protein coding sequences. Nodal support is given by posterior probabilities; branch-length scale indicates number of substitutions per site.

    Techniques Used:

    Sliding window analysis of complete mitochondrial genome sequences of xenopus frogs. The coloured lines show the value of nucleotide divergence K(JC) (average number of nucleotide substitutions per site between species with Jukes and Canor correction) in a sliding window analysis of window size 300 bp with step size 10 for: all four xenopus (black), ST v XL (green), ST v XB (light blue), ST v XV (dark blue), XL v XB (orange), XB v XV (turquoise) and XL and XV (red). Gene boundaries and primers and regions commonly used in DNA barcoding amphibians are indicated.
    Figure Legend Snippet: Sliding window analysis of complete mitochondrial genome sequences of xenopus frogs. The coloured lines show the value of nucleotide divergence K(JC) (average number of nucleotide substitutions per site between species with Jukes and Canor correction) in a sliding window analysis of window size 300 bp with step size 10 for: all four xenopus (black), ST v XL (green), ST v XB (light blue), ST v XV (dark blue), XL v XB (orange), XB v XV (turquoise) and XL and XV (red). Gene boundaries and primers and regions commonly used in DNA barcoding amphibians are indicated.

    Techniques Used:

    Long PCR, COX1, 16S, primer region 1 and primer region 2 amplicons. Agarose gel electrophoresis of ( A ) Xenopus borealis (XB; lanes 1 and 2) and X. victorianus (XV; lanes 3 and 4) PCR fragments using Long F1/R2 (lanes 1 and 3) and Long F2/R1 primers (lanes 2 and 4). ( B ) XB (lanes 1 and 2) and XV (lane 3) PCR fragments using COX1 (lane 1) and 16SA-Lmod/H (lanes 2 and 3) primers. ( C ) XB (lanes 1-2 and 5-6) and XV (lanes 3-4 and 7-8) PCR fragments using AMP1F/R (lanes 1-4) and AMP2F/R (lanes 5-8) primers. M1 and M2 = 1kb and 100bp DNA ladders, respectively.
    Figure Legend Snippet: Long PCR, COX1, 16S, primer region 1 and primer region 2 amplicons. Agarose gel electrophoresis of ( A ) Xenopus borealis (XB; lanes 1 and 2) and X. victorianus (XV; lanes 3 and 4) PCR fragments using Long F1/R2 (lanes 1 and 3) and Long F2/R1 primers (lanes 2 and 4). ( B ) XB (lanes 1 and 2) and XV (lane 3) PCR fragments using COX1 (lane 1) and 16SA-Lmod/H (lanes 2 and 3) primers. ( C ) XB (lanes 1-2 and 5-6) and XV (lanes 3-4 and 7-8) PCR fragments using AMP1F/R (lanes 1-4) and AMP2F/R (lanes 5-8) primers. M1 and M2 = 1kb and 100bp DNA ladders, respectively.

    Techniques Used: Polymerase Chain Reaction, Agarose Gel Electrophoresis

    9) Product Images from "The effects of vitamin D supplementation on metabolic profiles and gene expression of insulin and lipid metabolism in infertile polycystic ovary syndrome candidates for in vitro fertilization"

    Article Title: The effects of vitamin D supplementation on metabolic profiles and gene expression of insulin and lipid metabolism in infertile polycystic ovary syndrome candidates for in vitro fertilization

    Journal: Reproductive Biology and Endocrinology : RB & E

    doi: 10.1186/s12958-018-0413-3

    Effect of 8-week supplementation with vitamin D or placebo on expression ratio of PPAR-γ, GLUT-1 and LDLR gene in PBMCs of infertile women with polycystic ovary syndrome who were candidate for in vitro fertilization . GLUT-1, glucose transporter 1; LDLR, low-density lipoprotein receptor; PBMCs, peripheral blood mononuclear cells; PPAR-γ, peroxisome proliferator-activated receptor gamma
    Figure Legend Snippet: Effect of 8-week supplementation with vitamin D or placebo on expression ratio of PPAR-γ, GLUT-1 and LDLR gene in PBMCs of infertile women with polycystic ovary syndrome who were candidate for in vitro fertilization . GLUT-1, glucose transporter 1; LDLR, low-density lipoprotein receptor; PBMCs, peripheral blood mononuclear cells; PPAR-γ, peroxisome proliferator-activated receptor gamma

    Techniques Used: Expressing, In Vitro

    10) Product Images from "Human papillomavirus in premalignant oral lesions: No evidence of association in a Spanish cohort"

    Article Title: Human papillomavirus in premalignant oral lesions: No evidence of association in a Spanish cohort

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0210070

    Pictures of HE and p16 INK4a IHC of 3 out 4 HPV-DNA positive cases. Patient 1. (10X) Severe dysplasia at HE stain, HPV16 positivity and 26–50% staining for p16. Patient 2. (10X) Oral lichen planus at HE stain, HPV 16 positivity and negative staining for p16. Patient 3. (10X) Moderate dysplasia at HE stain, HPV18 positivity and 26–50% staining for p16. HE: hematoxilyn and eosin stain.
    Figure Legend Snippet: Pictures of HE and p16 INK4a IHC of 3 out 4 HPV-DNA positive cases. Patient 1. (10X) Severe dysplasia at HE stain, HPV16 positivity and 26–50% staining for p16. Patient 2. (10X) Oral lichen planus at HE stain, HPV 16 positivity and negative staining for p16. Patient 3. (10X) Moderate dysplasia at HE stain, HPV18 positivity and 26–50% staining for p16. HE: hematoxilyn and eosin stain.

    Techniques Used: Immunohistochemistry, H&E Stain, Staining, Negative Staining

    11) Product Images from "The effects of vitamin D supplementation on metabolic profiles and gene expression of insulin and lipid metabolism in infertile polycystic ovary syndrome candidates for in vitro fertilization"

    Article Title: The effects of vitamin D supplementation on metabolic profiles and gene expression of insulin and lipid metabolism in infertile polycystic ovary syndrome candidates for in vitro fertilization

    Journal: Reproductive Biology and Endocrinology : RB & E

    doi: 10.1186/s12958-018-0413-3

    Effect of 8-week supplementation with vitamin D or placebo on expression ratio of PPAR-γ, GLUT-1 and LDLR gene in PBMCs of infertile women with polycystic ovary syndrome who were candidate for in vitro fertilization . GLUT-1, glucose transporter 1; LDLR, low-density lipoprotein receptor; PBMCs, peripheral blood mononuclear cells; PPAR-γ, peroxisome proliferator-activated receptor gamma
    Figure Legend Snippet: Effect of 8-week supplementation with vitamin D or placebo on expression ratio of PPAR-γ, GLUT-1 and LDLR gene in PBMCs of infertile women with polycystic ovary syndrome who were candidate for in vitro fertilization . GLUT-1, glucose transporter 1; LDLR, low-density lipoprotein receptor; PBMCs, peripheral blood mononuclear cells; PPAR-γ, peroxisome proliferator-activated receptor gamma

    Techniques Used: Expressing, In Vitro

    12) Product Images from "Use of bexB To Detect the Capsule Locus in Haemophilus influenzae ▿"

    Article Title: Use of bexB To Detect the Capsule Locus in Haemophilus influenzae ▿

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.02509-10

    Schematic representations of the capsule locus. (A) The capsule locus can be categorized based upon its location in the H. influenzae genome relative to either an IS 1016 element or sodC . In one arrangement, the cap locus is flanked by IS 1016 insertion
    Figure Legend Snippet: Schematic representations of the capsule locus. (A) The capsule locus can be categorized based upon its location in the H. influenzae genome relative to either an IS 1016 element or sodC . In one arrangement, the cap locus is flanked by IS 1016 insertion

    Techniques Used:

    Suggested workflow for characterizing H. influenzae strain collections with regard to the capsule locus. Gene names listed within an oval represent detection of that gene via a PCR- or probe-based technique. Identification of “true” NTHI
    Figure Legend Snippet: Suggested workflow for characterizing H. influenzae strain collections with regard to the capsule locus. Gene names listed within an oval represent detection of that gene via a PCR- or probe-based technique. Identification of “true” NTHI

    Techniques Used: Polymerase Chain Reaction

    13) Product Images from "The Effects of Chromium Supplementation on Gene Expression of Insulin, Lipid, and Inflammatory Markers in Infertile Women With Polycystic Ovary Syndrome Candidate for in vitro Fertilization: A Randomized, Double-Blinded, Placebo-Controlled Trial"

    Article Title: The Effects of Chromium Supplementation on Gene Expression of Insulin, Lipid, and Inflammatory Markers in Infertile Women With Polycystic Ovary Syndrome Candidate for in vitro Fertilization: A Randomized, Double-Blinded, Placebo-Controlled Trial

    Journal: Frontiers in Endocrinology

    doi: 10.3389/fendo.2018.00726

    Fold change (means ± SDs) in gene expression levels of PPAR-γ, GLUT-1, and LDLR in women diagnosed with polycystic ovary syndrome who were candidate for in vitro fertilization, receiving chromium supplements and placebo. P -value was obtained from independent t -test. N = 20 in each group. IL-1, interleukin-1; IL-8, interleukin-8; LDLR, oxidized low-density lipoprotein receptor; PPAR-γ, peroxisome proliferator-activated receptor gamma; TNF-α, tumor necrosis factor alpha; TGF-β, transforming growth factor beta; VEGF, vascular endothelial growth factor.
    Figure Legend Snippet: Fold change (means ± SDs) in gene expression levels of PPAR-γ, GLUT-1, and LDLR in women diagnosed with polycystic ovary syndrome who were candidate for in vitro fertilization, receiving chromium supplements and placebo. P -value was obtained from independent t -test. N = 20 in each group. IL-1, interleukin-1; IL-8, interleukin-8; LDLR, oxidized low-density lipoprotein receptor; PPAR-γ, peroxisome proliferator-activated receptor gamma; TNF-α, tumor necrosis factor alpha; TGF-β, transforming growth factor beta; VEGF, vascular endothelial growth factor.

    Techniques Used: Expressing, In Vitro

    Change (means ± SDs) in gene expression levels of IL-1, IL-8, TNF-α, TGF-β, and VEGF in women diagnosed with polycystic ovary syndrome who were candidate for in vitro fertilization, receiving chromium supplements and placebo. P- value was obtained from independent t -test. N = 20 in each group. IL-1, interleukin-1; IL-8, interleukin-8; LDLR, oxidized low-density lipoprotein receptor; PPAR-γ, peroxisome proliferator-activated receptor gamma; TNF-α, tumor necrosis factor alpha; TGF-β, transforming growth factor beta; VEGF, vascular endothelial growth factor.
    Figure Legend Snippet: Change (means ± SDs) in gene expression levels of IL-1, IL-8, TNF-α, TGF-β, and VEGF in women diagnosed with polycystic ovary syndrome who were candidate for in vitro fertilization, receiving chromium supplements and placebo. P- value was obtained from independent t -test. N = 20 in each group. IL-1, interleukin-1; IL-8, interleukin-8; LDLR, oxidized low-density lipoprotein receptor; PPAR-γ, peroxisome proliferator-activated receptor gamma; TNF-α, tumor necrosis factor alpha; TGF-β, transforming growth factor beta; VEGF, vascular endothelial growth factor.

    Techniques Used: Expressing, In Vitro

    14) Product Images from "Human papillomavirus in premalignant oral lesions: No evidence of association in a Spanish cohort"

    Article Title: Human papillomavirus in premalignant oral lesions: No evidence of association in a Spanish cohort

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0210070

    Pictures of HE and p16 INK4a IHC of 3 out 4 HPV-DNA positive cases. Patient 1. (10X) Severe dysplasia at HE stain, HPV16 positivity and 26–50% staining for p16. Patient 2. (10X) Oral lichen planus at HE stain, HPV 16 positivity and negative staining for p16. Patient 3. (10X) Moderate dysplasia at HE stain, HPV18 positivity and 26–50% staining for p16. HE: hematoxilyn and eosin stain.
    Figure Legend Snippet: Pictures of HE and p16 INK4a IHC of 3 out 4 HPV-DNA positive cases. Patient 1. (10X) Severe dysplasia at HE stain, HPV16 positivity and 26–50% staining for p16. Patient 2. (10X) Oral lichen planus at HE stain, HPV 16 positivity and negative staining for p16. Patient 3. (10X) Moderate dysplasia at HE stain, HPV18 positivity and 26–50% staining for p16. HE: hematoxilyn and eosin stain.

    Techniques Used: Immunohistochemistry, H&E Stain, Staining, Negative Staining

    15) Product Images from "The Distribution and Identity of Edaphic Fungi in the McMurdo Dry Valleys"

    Article Title: The Distribution and Identity of Edaphic Fungi in the McMurdo Dry Valleys

    Journal: Biology

    doi: 10.3390/biology3030466

    Nonmetric multidimensional scaling (MDS) plot based on Bray-Curtis similarities of tRFLP profiles. Samples used for 454 PCR amplicon pyrosequencing are labeled by name. Significant correlations (Pearson R > 0.25) between plot ordinations and soil physicochemical properties are represented as vectors in gray.
    Figure Legend Snippet: Nonmetric multidimensional scaling (MDS) plot based on Bray-Curtis similarities of tRFLP profiles. Samples used for 454 PCR amplicon pyrosequencing are labeled by name. Significant correlations (Pearson R > 0.25) between plot ordinations and soil physicochemical properties are represented as vectors in gray.

    Techniques Used: Terminal Restriction Fragment Length Polymorphism, Polymerase Chain Reaction, Amplification, Labeling

    16) Product Images from "Microarray and Functional Analysis of Growth Phase-Dependent Gene Regulation in Bordetella bronchiseptica "

    Article Title: Microarray and Functional Analysis of Growth Phase-Dependent Gene Regulation in Bordetella bronchiseptica

    Journal: Infection and Immunity

    doi: 10.1128/IAI.00136-09

    Growth curves and changes in gene expression of genes that are negatively regulated by BvgAS and maximally expressed when the BvgAS system is inactive for B. bronchiseptica strain RB54, a Bvg − phase-locked mutant. (A) Optical densities (OD 600 ), DNA concentrations (geq/ml), and CFU counts (CFU/ml) during growth of RB50 are plotted along the y axis, and time, given in hours, is plotted along the x axis. All data points represent averages obtained from triplicate cultures. (B) Change in gene expression ( y axis) occurring at 6-h intervals ( x axis) starting at early logarithmic phase (12 h) and continuing until late stationary phase (48 h) determined by using qRT-PCR. Data shown are averages obtained from triplicate cultures. The error bars represent standard deviations.
    Figure Legend Snippet: Growth curves and changes in gene expression of genes that are negatively regulated by BvgAS and maximally expressed when the BvgAS system is inactive for B. bronchiseptica strain RB54, a Bvg − phase-locked mutant. (A) Optical densities (OD 600 ), DNA concentrations (geq/ml), and CFU counts (CFU/ml) during growth of RB50 are plotted along the y axis, and time, given in hours, is plotted along the x axis. All data points represent averages obtained from triplicate cultures. (B) Change in gene expression ( y axis) occurring at 6-h intervals ( x axis) starting at early logarithmic phase (12 h) and continuing until late stationary phase (48 h) determined by using qRT-PCR. Data shown are averages obtained from triplicate cultures. The error bars represent standard deviations.

    Techniques Used: Expressing, Mutagenesis, Quantitative RT-PCR

    Growth curves and changes in virulence gene expression of B. bronchiseptica strain RB50. (A) DNA concentrations (geq/ml) and CFU counts (CFU/ml) during growth of RB50 are plotted along the left y axis; optical densities (OD 600 ) are plotted along the right y axis; and time, given in hours, is plotted along the x axis. All data points represent averages obtained from triplicate cultures. (B) Change in gene expression ( y axis) occurring at 6-h intervals ( x axis), starting at early log phase (12 h) and continuing until late stationary phase (48 h), determined by using qRT-PCR. Data shown are averages obtained from triplicate cultures. The error bars represent standard deviations.
    Figure Legend Snippet: Growth curves and changes in virulence gene expression of B. bronchiseptica strain RB50. (A) DNA concentrations (geq/ml) and CFU counts (CFU/ml) during growth of RB50 are plotted along the left y axis; optical densities (OD 600 ) are plotted along the right y axis; and time, given in hours, is plotted along the x axis. All data points represent averages obtained from triplicate cultures. (B) Change in gene expression ( y axis) occurring at 6-h intervals ( x axis), starting at early log phase (12 h) and continuing until late stationary phase (48 h), determined by using qRT-PCR. Data shown are averages obtained from triplicate cultures. The error bars represent standard deviations.

    Techniques Used: Expressing, Quantitative RT-PCR

    17) Product Images from "Comparative metagenomic and rRNA microbial diversity characterization using Archaeal and Bacterial synthetic communities"

    Article Title: Comparative metagenomic and rRNA microbial diversity characterization using Archaeal and Bacterial synthetic communities

    Journal: Environmental microbiology

    doi: 10.1111/1462-2920.12086

    Characterization of the Archaea-Bacteria community by 454-FLX-T (A) and Illumina-HighSeq (B) metagenomic sequencing. The accuracy of retrieving the known composition of the metagenome is indicated for each organism as a ratio of the observed genomic coverage
    Figure Legend Snippet: Characterization of the Archaea-Bacteria community by 454-FLX-T (A) and Illumina-HighSeq (B) metagenomic sequencing. The accuracy of retrieving the known composition of the metagenome is indicated for each organism as a ratio of the observed genomic coverage

    Techniques Used: Sequencing

    18) Product Images from "Adjusting microbiome profiles for differences in microbial load by spike-in bacteria"

    Article Title: Adjusting microbiome profiles for differences in microbial load by spike-in bacteria

    Journal: Microbiome

    doi: 10.1186/s40168-016-0175-0

    Procedural overview of proposed spike-in procedure and the spike-in-based calibration to total microbial load (SCML). The overview is divided into four sections: spike-in procedure and bacterial lysis (blue), DNA isolation, amplification and sequencing (yellow), pre-processing (red) and the actual spike-in-based calibration to microbial load (green). White-filled boxes depict procedural intermediates, while grey-filled boxes depict the different procedural steps. Each step is numbered. In the first step (1) whole cells of exogenous spike bacteria corresponding to a fixed number of 16S rDNA copies are added to homogenized microbiome samples. Bacterial lysis is performed on the resulting spiked samples (2). Metagenomic DNA is extracted from the lysates (3) and PCR amplified using 16S rDNA specific primers (4), creating 16S rDNA amplicons. These amplicons are purified and pyrosequencing is performed (5). The resulting raw read counts are pre-processed with QIIME (quality filtering, demultiplexing and closed reference OTU picking) to generate OTU read count tables (6). Based on the read counts associated with single or multiple reference spike-in bacteria, a size factor s i for each sample i is calculated and applied to each OTU of this particular sample i (8, see methods section). This leads to an OTU read count table calibrated to differences in microbial load. These read counts can be utilized to more accurately assess changes between different samples. All depicted steps are described in detail in the methods section. Stars indicate points in the procedure at which qPCR is performed to identify possible errors in DNA isolation (metagenomic DNA) or PCR amplification (16S rDNA amplicons).
    Figure Legend Snippet: Procedural overview of proposed spike-in procedure and the spike-in-based calibration to total microbial load (SCML). The overview is divided into four sections: spike-in procedure and bacterial lysis (blue), DNA isolation, amplification and sequencing (yellow), pre-processing (red) and the actual spike-in-based calibration to microbial load (green). White-filled boxes depict procedural intermediates, while grey-filled boxes depict the different procedural steps. Each step is numbered. In the first step (1) whole cells of exogenous spike bacteria corresponding to a fixed number of 16S rDNA copies are added to homogenized microbiome samples. Bacterial lysis is performed on the resulting spiked samples (2). Metagenomic DNA is extracted from the lysates (3) and PCR amplified using 16S rDNA specific primers (4), creating 16S rDNA amplicons. These amplicons are purified and pyrosequencing is performed (5). The resulting raw read counts are pre-processed with QIIME (quality filtering, demultiplexing and closed reference OTU picking) to generate OTU read count tables (6). Based on the read counts associated with single or multiple reference spike-in bacteria, a size factor s i for each sample i is calculated and applied to each OTU of this particular sample i (8, see methods section). This leads to an OTU read count table calibrated to differences in microbial load. These read counts can be utilized to more accurately assess changes between different samples. All depicted steps are described in detail in the methods section. Stars indicate points in the procedure at which qPCR is performed to identify possible errors in DNA isolation (metagenomic DNA) or PCR amplification (16S rDNA amplicons).

    Techniques Used: Lysis, DNA Extraction, Amplification, Sequencing, Polymerase Chain Reaction, Purification, Real-time Polymerase Chain Reaction

    Comparison of SCML and normalization by qRT-PCR-derived total number of 16S rDNA copies to all background OTUs. Observed log 2 ratio versus expected log 2 ratio of all background bacteria OTUs for all pairwise sample comparisons after ( a ) SCML by S. ruber and ( b ) normalization by qRT-PCR derived total 16S rDNA copy number. The data is binned to hexagons because of the high number of data points. The colour of each hexagon represents the percentage of all counts at the corresponding level of expected log 2 ratios contained in each bin. Bins that contributed to less than 0.05 percent for each level of expected log 2 ratio are omitted. The purple diagonal represents the identity, which represents the expected log 2 ratios by design. The box-plots in ( c ) summarize the error between the expected and observed log 2 ratios for the four different approaches. The smaller this error, the better calibrated the ratios are. Variances of the log 2 differences are 3.65, 2.01, 1.28 and 1.18 as derived from relative abundances, counts calibrated for differences in total number of 16S rRNA gene copies, SCML (by S. ruber ) and combined SCML (by S. ruber , A. acidiphilus and R. radiobacter ), respectively
    Figure Legend Snippet: Comparison of SCML and normalization by qRT-PCR-derived total number of 16S rDNA copies to all background OTUs. Observed log 2 ratio versus expected log 2 ratio of all background bacteria OTUs for all pairwise sample comparisons after ( a ) SCML by S. ruber and ( b ) normalization by qRT-PCR derived total 16S rDNA copy number. The data is binned to hexagons because of the high number of data points. The colour of each hexagon represents the percentage of all counts at the corresponding level of expected log 2 ratios contained in each bin. Bins that contributed to less than 0.05 percent for each level of expected log 2 ratio are omitted. The purple diagonal represents the identity, which represents the expected log 2 ratios by design. The box-plots in ( c ) summarize the error between the expected and observed log 2 ratios for the four different approaches. The smaller this error, the better calibrated the ratios are. Variances of the log 2 differences are 3.65, 2.01, 1.28 and 1.18 as derived from relative abundances, counts calibrated for differences in total number of 16S rRNA gene copies, SCML (by S. ruber ) and combined SCML (by S. ruber , A. acidiphilus and R. radiobacter ), respectively

    Techniques Used: Quantitative RT-PCR, Derivative Assay

    19) Product Images from "Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform"

    Article Title: Analysis of 16S rRNA Amplicon Sequencing Options on the Roche/454 Next-Generation Titanium Sequencing Platform

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0025263

    Experimental design showing three methods for 16S pyrotag sequencing. MID stands for multiplex identifier sequence for differentiation of multiplex sequence data sets. Method-1 was performed using LIB-A kit with a primer set of FA-MID-515F and FB-909R. Method-2 was done by LIB-A kit with two primer sets of FA-MID-515F and FB-909R and FB-MID-515F and FA-909R. Method-3 was done using LIB-L kit with a primer set of FA′-MID-515F and FB′-909R.
    Figure Legend Snippet: Experimental design showing three methods for 16S pyrotag sequencing. MID stands for multiplex identifier sequence for differentiation of multiplex sequence data sets. Method-1 was performed using LIB-A kit with a primer set of FA-MID-515F and FB-909R. Method-2 was done by LIB-A kit with two primer sets of FA-MID-515F and FB-909R and FB-MID-515F and FA-909R. Method-3 was done using LIB-L kit with a primer set of FA′-MID-515F and FB′-909R.

    Techniques Used: Sequencing, Multiplex Assay

    20) Product Images from "Gonococcal Porin IB Activates NF-?B in Human Urethral Epithelium and Increases the Expression of Host Antiapoptotic Factors "

    Article Title: Gonococcal Porin IB Activates NF-?B in Human Urethral Epithelium and Increases the Expression of Host Antiapoptotic Factors

    Journal: Infection and Immunity

    doi: 10.1128/IAI.72.11.6408-6417.2004

    Increased expression of bfl-1 in urethral epithelium infected with live or gentamicin-killed N. gonorrhoeae . UECs received medium alone (uninfected) or were challenged for 4 h with live (1291) or gentamicin-killed (1291+Gent) gonococci. After infection, total RNA was harvested, and cDNA was synthesized. PCR analysis then demonstrated that expression of the antiapoptotic Bcl-2 family member bfl-1 is increased in UECs infected with either live or gentamicin-killed gonococci. Panel 1, 18S rRNA internal control; panel 2, bfl-1 ; panel 3, reverse transcriptase-negative controls.
    Figure Legend Snippet: Increased expression of bfl-1 in urethral epithelium infected with live or gentamicin-killed N. gonorrhoeae . UECs received medium alone (uninfected) or were challenged for 4 h with live (1291) or gentamicin-killed (1291+Gent) gonococci. After infection, total RNA was harvested, and cDNA was synthesized. PCR analysis then demonstrated that expression of the antiapoptotic Bcl-2 family member bfl-1 is increased in UECs infected with either live or gentamicin-killed gonococci. Panel 1, 18S rRNA internal control; panel 2, bfl-1 ; panel 3, reverse transcriptase-negative controls.

    Techniques Used: Expressing, Infection, Synthesized, Polymerase Chain Reaction

    21) Product Images from "Comparative metagenomic and rRNA microbial diversity characterization using Archaeal and Bacterial synthetic communities"

    Article Title: Comparative metagenomic and rRNA microbial diversity characterization using Archaeal and Bacterial synthetic communities

    Journal: Environmental microbiology

    doi: 10.1111/1462-2920.12086

    ( A ) Principal Coordinate Analysis (Bray-Curtis similarity) of Bacteria and Archaea community composition inferred using metagenomics (454-M and ILM-M) and SSU rDNA amplicon sequencing relative to the known composition based on community assembly (REF).
    Figure Legend Snippet: ( A ) Principal Coordinate Analysis (Bray-Curtis similarity) of Bacteria and Archaea community composition inferred using metagenomics (454-M and ILM-M) and SSU rDNA amplicon sequencing relative to the known composition based on community assembly (REF).

    Techniques Used: Amplification, Sequencing

    OTU-based diversity estimation as a function of genetic distance and analytical approach relative to the reference genomic SSU rRNA sequences. Bacterial V13, V4, archaeal V13 and the combined archaeal-bacterial V48 amplicon datasets are shown. The results
    Figure Legend Snippet: OTU-based diversity estimation as a function of genetic distance and analytical approach relative to the reference genomic SSU rRNA sequences. Bacterial V13, V4, archaeal V13 and the combined archaeal-bacterial V48 amplicon datasets are shown. The results

    Techniques Used: Amplification

    Taxonomic diversity and abundance inferences based on shotgun metagenomic and amplicon sequencing. The accuracy ratio (observed abundance/expected abundance) is represented as a heat map diagram with values for each organism and data set. Bias values
    Figure Legend Snippet: Taxonomic diversity and abundance inferences based on shotgun metagenomic and amplicon sequencing. The accuracy ratio (observed abundance/expected abundance) is represented as a heat map diagram with values for each organism and data set. Bias values

    Techniques Used: Amplification, Sequencing

    22) Product Images from "Role of Cellular Heparan Sulfate Proteoglycans in Infection of Human Adenovirus Serotype 3 and 35"

    Article Title: Role of Cellular Heparan Sulfate Proteoglycans in Infection of Human Adenovirus Serotype 3 and 35

    Journal: PLoS Pathogens

    doi: 10.1371/journal.ppat.1000189

    Sulfation of HSPGs is essential for interaction with Ad3 fiber knob. (A) Glycan binding specificity of Ad3 and Ad35 knob on glycan array. The plot shows the average relative fluorescence units (RFU; y -axis) for the six addresses of each glycan versus glycan number ( x -axis) as bars. Standard deviations in the fluorescence for the six addresses are indicated for each glycan. Sulfated glycans are indicated with black bars. Arrows indicate glycan#26. (B) Ad3 and Ad35 knob binding specificity to sulfated glycans on glycan array. For structure of sulfated glycans see Table 1 . (C) Ad3 and Ad35 knob binding to CHO-K1 and CHO-pgsE-606 cells. (D) Binding of anti-HSPG antibody to CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells. (C,D) Bars represent the mean and standard deviation of experiments performed in triplicate. These experiments were independently repeated once with a similar outcome.
    Figure Legend Snippet: Sulfation of HSPGs is essential for interaction with Ad3 fiber knob. (A) Glycan binding specificity of Ad3 and Ad35 knob on glycan array. The plot shows the average relative fluorescence units (RFU; y -axis) for the six addresses of each glycan versus glycan number ( x -axis) as bars. Standard deviations in the fluorescence for the six addresses are indicated for each glycan. Sulfated glycans are indicated with black bars. Arrows indicate glycan#26. (B) Ad3 and Ad35 knob binding specificity to sulfated glycans on glycan array. For structure of sulfated glycans see Table 1 . (C) Ad3 and Ad35 knob binding to CHO-K1 and CHO-pgsE-606 cells. (D) Binding of anti-HSPG antibody to CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells. (C,D) Bars represent the mean and standard deviation of experiments performed in triplicate. These experiments were independently repeated once with a similar outcome.

    Techniques Used: Binding Assay, Fluorescence, Standard Deviation

    Effect of HSPG-expression and HSPG-sulfation on Ad3 and Ad35 virus particle attachment to cells. (A) Trypsin and EDTA competition of Ad3 and Ad35 knob binding to HeLa cells. (B) Trypsin and EDTA competition of Ad3 and Ad35 virus particle binding to HeLa cells. (C) Heparin competition of Ad3 and Ad35 virus particle binding to HeLa cells. (D) Heparinase competition of Ad3 and Ad35 virus particle binding to HeLa and Y79 cells. (E) EDTA competition of Ad3 virus particle binding to CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells. Bars represent the mean and standard deviation of experiments performed in triplicate. All experiments were independently repeated at least once with a similar outcome.
    Figure Legend Snippet: Effect of HSPG-expression and HSPG-sulfation on Ad3 and Ad35 virus particle attachment to cells. (A) Trypsin and EDTA competition of Ad3 and Ad35 knob binding to HeLa cells. (B) Trypsin and EDTA competition of Ad3 and Ad35 virus particle binding to HeLa cells. (C) Heparin competition of Ad3 and Ad35 virus particle binding to HeLa cells. (D) Heparinase competition of Ad3 and Ad35 virus particle binding to HeLa and Y79 cells. (E) EDTA competition of Ad3 virus particle binding to CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells. Bars represent the mean and standard deviation of experiments performed in triplicate. All experiments were independently repeated at least once with a similar outcome.

    Techniques Used: Expressing, Binding Assay, Standard Deviation

    Ad3 but not Ad35 fiber knob interacts with cellular HSPGs. (A) Competition of Ad3 and Ad35 virus particle attachment to HeLa cells using pre-incubation of cells with increasing concentrations of the corresponding knob proteins. (B) Ad3 and Ad35 fiber knob binding to HeLa cells. Note that Ad35 but not Ad3 knob reached saturation of available receptors (for representative flow charts see Figure S2 ). (C) Ad3 and Ad35 knob binding to CHO-K1 and CHO-C2 cells. (D) Heparin competition of Ad3 and Ad35 knob binding to HeLa cells. (E) Heparinase competition of Ad3 and Ad35 knob binding to HeLa, CHO-C2, and Y79 cells. (F) Ad3 knob binding to CHO-K1 and CHO-pgsA-745 cells. (G) Ad3 and Ad35 knob and virus particle binding to Ramos cells. (H) Ad3 and Ad35 knob binding to Heparin and soluble CD46 assessed via western blot. (A–G) Data points represent the mean and standard deviation of experiments performed in triplicate. All experiments were independently repeated at least once with a similar outcome.
    Figure Legend Snippet: Ad3 but not Ad35 fiber knob interacts with cellular HSPGs. (A) Competition of Ad3 and Ad35 virus particle attachment to HeLa cells using pre-incubation of cells with increasing concentrations of the corresponding knob proteins. (B) Ad3 and Ad35 fiber knob binding to HeLa cells. Note that Ad35 but not Ad3 knob reached saturation of available receptors (for representative flow charts see Figure S2 ). (C) Ad3 and Ad35 knob binding to CHO-K1 and CHO-C2 cells. (D) Heparin competition of Ad3 and Ad35 knob binding to HeLa cells. (E) Heparinase competition of Ad3 and Ad35 knob binding to HeLa, CHO-C2, and Y79 cells. (F) Ad3 knob binding to CHO-K1 and CHO-pgsA-745 cells. (G) Ad3 and Ad35 knob and virus particle binding to Ramos cells. (H) Ad3 and Ad35 knob binding to Heparin and soluble CD46 assessed via western blot. (A–G) Data points represent the mean and standard deviation of experiments performed in triplicate. All experiments were independently repeated at least once with a similar outcome.

    Techniques Used: Incubation, Binding Assay, Flow Cytometry, Western Blot, Standard Deviation

    Model of HSPG-function in Ad3 and Ad35 infection of CHO cells. Ad3 and Ad35 infection of CHO cells expressing (i) sulfated HSPGs (CHO-K1), (ii) no HSPGs (CHO-pgsA-745), or (iii) non-sulfated HSPGs (CHO-pgsE-606). (A) Ad3 interacts via fiber knob with sulfated HSPGs (a), which facilitates infection via receptor X (co-receptor function of HSPGs) (b). Ad3 also directly interacts with receptor X (independent of HSPGs) (c). HSPGs that do not co-localize with receptor X also bind Ad3, which does not increase Ad3 infection (barrier function of sulfated HSPGs due to Ad3 binding) (d). (B) Absence of HSPG expression overall increases Ad3 infection. Ad3 directly interacts with receptor X. (C) Ad3 knob does not interact with non-sulfated HSPGs. This blocks Ad3 interaction with HSPGs. Non-sulfated HSPGs do not act as an Ad3 co-receptor. Non-sulfated HSPGs inhibit access of Ad3 to receptor X (physical barrier function of non-sulfated HSPGs). Consequently, Ad3 infection is decreased in CHO-pgsE-606 cells. (D) Ad35 utilizes sulfated HSPGs as alternative low-affinity receptors in the absence of the high-affinity receptor CD46. This mediates infection of CD46-negative CHO cells (receptor function of HSPGs). Absence of HSPG expression (E) and absence of HSPG sulfation (F) strongly decreases Ad35 infection (loss of HSPG receptor function).
    Figure Legend Snippet: Model of HSPG-function in Ad3 and Ad35 infection of CHO cells. Ad3 and Ad35 infection of CHO cells expressing (i) sulfated HSPGs (CHO-K1), (ii) no HSPGs (CHO-pgsA-745), or (iii) non-sulfated HSPGs (CHO-pgsE-606). (A) Ad3 interacts via fiber knob with sulfated HSPGs (a), which facilitates infection via receptor X (co-receptor function of HSPGs) (b). Ad3 also directly interacts with receptor X (independent of HSPGs) (c). HSPGs that do not co-localize with receptor X also bind Ad3, which does not increase Ad3 infection (barrier function of sulfated HSPGs due to Ad3 binding) (d). (B) Absence of HSPG expression overall increases Ad3 infection. Ad3 directly interacts with receptor X. (C) Ad3 knob does not interact with non-sulfated HSPGs. This blocks Ad3 interaction with HSPGs. Non-sulfated HSPGs do not act as an Ad3 co-receptor. Non-sulfated HSPGs inhibit access of Ad3 to receptor X (physical barrier function of non-sulfated HSPGs). Consequently, Ad3 infection is decreased in CHO-pgsE-606 cells. (D) Ad35 utilizes sulfated HSPGs as alternative low-affinity receptors in the absence of the high-affinity receptor CD46. This mediates infection of CD46-negative CHO cells (receptor function of HSPGs). Absence of HSPG expression (E) and absence of HSPG sulfation (F) strongly decreases Ad35 infection (loss of HSPG receptor function).

    Techniques Used: Infection, Expressing, Binding Assay, Activated Clotting Time Assay

    Effect of HSPG-expression and HSPG-sulfation on Ad35 infection of CHO cells. (A) Hexon staining. CHO-K1 cells were infected with Ad35 (MOI 2560 pfu/cell). Three days post-infection, cells were fixed and stained for adenovirus hexon protein (red), E-cadherin as a cell surface marker (green), and nuclei (DAPI, blue). Magnification 40×. (B) MTT assay. CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells were infected with an increasing MOI of Ad35 (0, 640, 1280, 2560, 5120, 10240 pfu/cell). Seven days post-infection, mitochondrial activity of cells was determined via MTT assay. Data points represent the mean and standard deviation of experiments performed in triplicate. (C) CPE assay. CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells were infected with Ad35 in a range of 0–20480 pfu/cell and monitored for CPE as described in Materials and Methods . Five days post-infection, cells were fixed and stained with crystal violet. Representative pictures are shown. Upper row: Photographs of crystal violet stained wells. Lower row: Photographs (Magnification 40×) of crystal violet stained wells. Presence of CPE is indicated with black borderlines. (D) Ad35 viral replication assay. Fold increase of Ad35 viral genomes 5 days post-infection of CHO-K1, CHO-pgsA-745, CHO-pgsE-606, and A549 cells is shown. Bars represent the mean and standard deviation of experiments performed in duplicate. (B–D) These experiments were independently repeated twice with similar outcomes.
    Figure Legend Snippet: Effect of HSPG-expression and HSPG-sulfation on Ad35 infection of CHO cells. (A) Hexon staining. CHO-K1 cells were infected with Ad35 (MOI 2560 pfu/cell). Three days post-infection, cells were fixed and stained for adenovirus hexon protein (red), E-cadherin as a cell surface marker (green), and nuclei (DAPI, blue). Magnification 40×. (B) MTT assay. CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells were infected with an increasing MOI of Ad35 (0, 640, 1280, 2560, 5120, 10240 pfu/cell). Seven days post-infection, mitochondrial activity of cells was determined via MTT assay. Data points represent the mean and standard deviation of experiments performed in triplicate. (C) CPE assay. CHO-K1, CHO-pgsA-745, and CHO-pgsE-606 cells were infected with Ad35 in a range of 0–20480 pfu/cell and monitored for CPE as described in Materials and Methods . Five days post-infection, cells were fixed and stained with crystal violet. Representative pictures are shown. Upper row: Photographs of crystal violet stained wells. Lower row: Photographs (Magnification 40×) of crystal violet stained wells. Presence of CPE is indicated with black borderlines. (D) Ad35 viral replication assay. Fold increase of Ad35 viral genomes 5 days post-infection of CHO-K1, CHO-pgsA-745, CHO-pgsE-606, and A549 cells is shown. Bars represent the mean and standard deviation of experiments performed in duplicate. (B–D) These experiments were independently repeated twice with similar outcomes.

    Techniques Used: Expressing, Infection, Staining, Marker, MTT Assay, Activity Assay, Standard Deviation, Viral Replication Assay

    23) Product Images from "Coamplification of HIV-1 Proviral DNA and Viral RNA in Assays Used for Quantification of HIV-1 RNA ▿"

    Article Title: Coamplification of HIV-1 Proviral DNA and Viral RNA in Assays Used for Quantification of HIV-1 RNA ▿

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.02034-09

    Densitometric analysis of amplified β-globin DNA in nucleic acid extracted from EDTA and PPT plasma specimens. ΔEDTA and ΔPPT represent extracted specimens that were heat inactivated for removal of RNA.
    Figure Legend Snippet: Densitometric analysis of amplified β-globin DNA in nucleic acid extracted from EDTA and PPT plasma specimens. ΔEDTA and ΔPPT represent extracted specimens that were heat inactivated for removal of RNA.

    Techniques Used: Amplification

    24) Product Images from "Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle"

    Article Title: Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0073827

    Rarefaction, richness, and diversity analyses of 16s amplicon data. Approximately 166 bacterial OTUs were detected through amplicon sequencing. Various community richness estimators consistently predicted the presence of over 300 OTUs in association with the A . glabripennis gut and, in agreement with this observation, the rarefaction curve failed to reach saturation. This indicates that additional OTUs would likely be detected with additional amplicon sequencing.
    Figure Legend Snippet: Rarefaction, richness, and diversity analyses of 16s amplicon data. Approximately 166 bacterial OTUs were detected through amplicon sequencing. Various community richness estimators consistently predicted the presence of over 300 OTUs in association with the A . glabripennis gut and, in agreement with this observation, the rarefaction curve failed to reach saturation. This indicates that additional OTUs would likely be detected with additional amplicon sequencing.

    Techniques Used: Amplification, Sequencing

    Rarefaction, richness, and diversity analyses of 18S amplicon data. Seven fungal OTUs were detected through amplicon sequencing. While rarefaction begins to approach saturation, richness estimates predict the presence of at least 11 fungal OTUs indicating that additional sampling may be necessary. This scenario is likely since additional 18S rRNAs from fungal taxa not detected in the 18S amplicons were detected in the shotgun reads (e.g., Fusarium spp.).
    Figure Legend Snippet: Rarefaction, richness, and diversity analyses of 18S amplicon data. Seven fungal OTUs were detected through amplicon sequencing. While rarefaction begins to approach saturation, richness estimates predict the presence of at least 11 fungal OTUs indicating that additional sampling may be necessary. This scenario is likely since additional 18S rRNAs from fungal taxa not detected in the 18S amplicons were detected in the shotgun reads (e.g., Fusarium spp.).

    Techniques Used: Amplification, Sequencing, Sampling

    25) Product Images from "Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1 [C]Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1 [C] [W]Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1 [C] [W] [OA]"

    Article Title: Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1 [C]Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1 [C] [W]Negative Feedback Control of Jasmonate Signaling by an Alternative Splice Variant of JAZ10 1 [C] [W] [OA]

    Journal: Plant Physiology

    doi: 10.1104/pp.113.218164

    JAZ10.4 Interacts with Basic Helix-Loop-Helix and NINJA
    Figure Legend Snippet: JAZ10.4 Interacts with Basic Helix-Loop-Helix and NINJA

    Techniques Used:

    of JAZ10.4. The indicated R→A substitution mutants of JAZ10.4 were tested for interaction with
    Figure Legend Snippet: of JAZ10.4. The indicated R→A substitution mutants of JAZ10.4 were tested for interaction with

    Techniques Used:

    JAZ10.4 Interacts with Basic Helix-Loop-Helix and NINJA
    Figure Legend Snippet: JAZ10.4 Interacts with Basic Helix-Loop-Helix and NINJA

    Techniques Used:

    responses. A, The photograph shows silique development in the wild type (WT) and transgenic lines that overexpress JAZ10.4 or JAZ10.4 RRR→AAA . B, The photograph shows seedlings
    Figure Legend Snippet: responses. A, The photograph shows silique development in the wild type (WT) and transgenic lines that overexpress JAZ10.4 or JAZ10.4 RRR→AAA . B, The photograph shows seedlings

    Techniques Used: Transgenic Assay

    assays depicting the interaction of JAZ10 or JAZ8 chimeric proteins (DNA binding-domain fusions [DB]) with MYC2, JAZ1, NINJA (NJA), and TPL (activation
    Figure Legend Snippet: assays depicting the interaction of JAZ10 or JAZ8 chimeric proteins (DNA binding-domain fusions [DB]) with MYC2, JAZ1, NINJA (NJA), and TPL (activation

    Techniques Used: Binding Assay, Activation Assay

    assays of JAZ10.4 deletion constructs (DNA-binding domain bait fusions) with MYC2 and JAZ10.4 (activation domain prey fusions). Yeast strains coexpressing the indicated bait
    Figure Legend Snippet: assays of JAZ10.4 deletion constructs (DNA-binding domain bait fusions) with MYC2 and JAZ10.4 (activation domain prey fusions). Yeast strains coexpressing the indicated bait

    Techniques Used: Construct, Binding Assay, Activation Assay

    -hypersensitive phenotype of jaz10-1 . A, Root growth inhibition assay of the wild type (WT), jaz10-1 ( jaz10 ), and five independent lines in which the pJAZ10 : HA-JAZ10.4 transgene was introduced into the
    Figure Legend Snippet: -hypersensitive phenotype of jaz10-1 . A, Root growth inhibition assay of the wild type (WT), jaz10-1 ( jaz10 ), and five independent lines in which the pJAZ10 : HA-JAZ10.4 transgene was introduced into the

    Techniques Used: Growth Inhibition Assay

    26) Product Images from "Strategy for Robust Detection of Insertions, Deletions, and Point Mutations in CEBPA, a GC-Rich Content Gene, Using 454 Next-Generation Deep-Sequencing Technology"

    Article Title: Strategy for Robust Detection of Insertions, Deletions, and Point Mutations in CEBPA, a GC-Rich Content Gene, Using 454 Next-Generation Deep-Sequencing Technology

    Journal: The Journal of Molecular Diagnostics : JMD

    doi: 10.1016/j.jmoldx.2010.09.001

    Sequencing coverage of the four CEBPA amplicons using standard GS FLX Titanium Sequencing emPCR conditions. For both patients T13 and T15, the number of obtained sequencing reads using the procedure as recommended by the manufacturer is given on the y
    Figure Legend Snippet: Sequencing coverage of the four CEBPA amplicons using standard GS FLX Titanium Sequencing emPCR conditions. For both patients T13 and T15, the number of obtained sequencing reads using the procedure as recommended by the manufacturer is given on the y

    Techniques Used: Sequencing

    Sequencing coverage of the four CEBPA amplicons using various emPCR conditions. For both patients T13 and T15, four distinct GS FLX Titanium Sequencing emPCR conditions were tested ( A–D ). The number of obtained sequencing reads is given on the
    Figure Legend Snippet: Sequencing coverage of the four CEBPA amplicons using various emPCR conditions. For both patients T13 and T15, four distinct GS FLX Titanium Sequencing emPCR conditions were tested ( A–D ). The number of obtained sequencing reads is given on the

    Techniques Used: Sequencing

    27) Product Images from "IGF2BP3 modulates the interaction of invasion-associated transcripts with RISC"

    Article Title: IGF2BP3 modulates the interaction of invasion-associated transcripts with RISC

    Journal: Cell reports

    doi: 10.1016/j.celrep.2016.04.083

    IGF2BP3 alters mRNA association with RISC A . Western blot of Ago2 immunoprecipitation from control (NT) or IGF2BP3-depleted (KD) PANC1 cells. (B–F) RT-qPCR analysis of RNA precipitated with α-Ago2 or nonspecific rabbit IgG (Ago2 RIP or IgG RIP, respectively). Relative quantification for each transcript was performed using 18S rRNA as a reference gene. Statistical significance was estimated for each comparison using an unpaired T-test (* P
    Figure Legend Snippet: IGF2BP3 alters mRNA association with RISC A . Western blot of Ago2 immunoprecipitation from control (NT) or IGF2BP3-depleted (KD) PANC1 cells. (B–F) RT-qPCR analysis of RNA precipitated with α-Ago2 or nonspecific rabbit IgG (Ago2 RIP or IgG RIP, respectively). Relative quantification for each transcript was performed using 18S rRNA as a reference gene. Statistical significance was estimated for each comparison using an unpaired T-test (* P

    Techniques Used: Western Blot, Immunoprecipitation, Quantitative RT-PCR

    28) Product Images from "The effects of vitamin D supplementation on metabolic profiles and gene expression of insulin and lipid metabolism in infertile polycystic ovary syndrome candidates for in vitro fertilization"

    Article Title: The effects of vitamin D supplementation on metabolic profiles and gene expression of insulin and lipid metabolism in infertile polycystic ovary syndrome candidates for in vitro fertilization

    Journal: Reproductive Biology and Endocrinology : RB & E

    doi: 10.1186/s12958-018-0413-3

    Effect of 8-week supplementation with vitamin D or placebo on expression ratio of PPAR-γ, GLUT-1 and LDLR gene in PBMCs of infertile women with polycystic ovary syndrome who were candidate for in vitro fertilization . GLUT-1, glucose transporter 1; LDLR, low-density lipoprotein receptor; PBMCs, peripheral blood mononuclear cells; PPAR-γ, peroxisome proliferator-activated receptor gamma
    Figure Legend Snippet: Effect of 8-week supplementation with vitamin D or placebo on expression ratio of PPAR-γ, GLUT-1 and LDLR gene in PBMCs of infertile women with polycystic ovary syndrome who were candidate for in vitro fertilization . GLUT-1, glucose transporter 1; LDLR, low-density lipoprotein receptor; PBMCs, peripheral blood mononuclear cells; PPAR-γ, peroxisome proliferator-activated receptor gamma

    Techniques Used: Expressing, In Vitro

    29) Product Images from "RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers"

    Article Title: RNase H-dependent PCR (rhPCR): improved specificity and single nucleotide polymorphism detection using blocked cleavable primers

    Journal: BMC Biotechnology

    doi: 10.1186/1472-6750-11-80

    Increased specificity of rhPCR with complex DNA samples . A PCR assay specific for the human HRAS gene was used to compare the specificity of
    Figure Legend Snippet: Increased specificity of rhPCR with complex DNA samples . A PCR assay specific for the human HRAS gene was used to compare the specificity of "rDDDDx" blocked-cleavable primers (rhPCR) with unmodified control primers to amplify the desired sequences in human cDNA versus mismatched sequences in rat cDNA. A. Amplification plots are shown for SYBR ® Green qPCR assays run with unmodified control primers (left panel) or blocked-cleavable primers (right panel). Reactions with human cDNA (HeLa) are shown in black and reactions with rat cDNA (spinal cord) are shown in blue. The concentration of RNase H2 was 1.3 mU per 10 μL and the anneal/extension time was 90 seconds. B. The human HRAS -specific amplification primers are shown aligned with the homologous sequence in the rat Hras gene. Unmodified control primers are shown on the left and blocked-cleavable primers are shown on the right. DNA bases are black uppercase and RNA bases are red lowercase. "x" is a propanediol C3 spacer.

    Techniques Used: RNase H-dependent PCR, Polymerase Chain Reaction, Amplification, SYBR Green Assay, Real-time Polymerase Chain Reaction, Concentration Assay, Sequencing

    30) Product Images from "Detection of HER-2/neu-positive circulating epithelial cells in prostate cancer patients"

    Article Title: Detection of HER-2/neu-positive circulating epithelial cells in prostate cancer patients

    Journal: British Journal of Cancer

    doi: 10.1038/sj.bjc.6601532

    Expression of HER-2/neu RNA by real-time PCR (LightCycler). Amplification curve shows serial dilutions of an initial amount of SK-BR-3 RNA: 1 (3333 cells), 2 (333 cells), 3 (166 cells), 4 (33 cells), 5 (16 cells), 6 (1.6 cells) and 7 (0.6 cells). Inset, standard curve plot of the log of SK-BR-3 RNA cells numbers vs Cp. The standard curve shows seven orders of linear dynamic range ( y =−3.67 x +33.071; R 2 =0.9983).
    Figure Legend Snippet: Expression of HER-2/neu RNA by real-time PCR (LightCycler). Amplification curve shows serial dilutions of an initial amount of SK-BR-3 RNA: 1 (3333 cells), 2 (333 cells), 3 (166 cells), 4 (33 cells), 5 (16 cells), 6 (1.6 cells) and 7 (0.6 cells). Inset, standard curve plot of the log of SK-BR-3 RNA cells numbers vs Cp. The standard curve shows seven orders of linear dynamic range ( y =−3.67 x +33.071; R 2 =0.9983).

    Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Amplification

    Carcinoma cells isolated with BerEP4-coated immunomagnetic beads from patient no. 34, coloration by May–Grünwald–Giemsa (CTCs isolated from a patient with localised prostate carcinoma before treatment by brachytherapy, this was an HER-2/neu-positive patient).
    Figure Legend Snippet: Carcinoma cells isolated with BerEP4-coated immunomagnetic beads from patient no. 34, coloration by May–Grünwald–Giemsa (CTCs isolated from a patient with localised prostate carcinoma before treatment by brachytherapy, this was an HER-2/neu-positive patient).

    Techniques Used: Isolation

    31) Product Images from "Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing"

    Article Title: Cilantro microbiome before and after nonselective pre-enrichment for Salmonella using 16S rRNA and metagenomic sequencing

    Journal: BMC Microbiology

    doi: 10.1186/s12866-015-0497-2

    a Sensitivity testing of the Enterobacteriaceae database. Randomly fragmented 16S rRNA genes specific to S. enterica were compared to the Enterobacteriaceae database using BLASTn. Fragment sizes ranged from 100 to 500 bp and errors were randomly introduced at rates ranging from 0 to 1 %. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S fragments without a Salmonella best alignment (right axis). b Specificity testing of the Enterobacteriaceae database. 16S rRNA fragments specific to E. coli were randomly fragmented to sizes ranging from 100 to 500 bp and random errors were introduced. Fragments were searched against the Enterobacteriaceae database using BLASTn. c Validation of the Enterobacteriaceae database using BLASTn analysis of raw Illumina MiSeq reads from 105 S. enterica 16S rRNA genes to the EnteroDB. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S rRNA fragments without a Salmonella best alignment (right axis)
    Figure Legend Snippet: a Sensitivity testing of the Enterobacteriaceae database. Randomly fragmented 16S rRNA genes specific to S. enterica were compared to the Enterobacteriaceae database using BLASTn. Fragment sizes ranged from 100 to 500 bp and errors were randomly introduced at rates ranging from 0 to 1 %. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S fragments without a Salmonella best alignment (right axis). b Specificity testing of the Enterobacteriaceae database. 16S rRNA fragments specific to E. coli were randomly fragmented to sizes ranging from 100 to 500 bp and random errors were introduced. Fragments were searched against the Enterobacteriaceae database using BLASTn. c Validation of the Enterobacteriaceae database using BLASTn analysis of raw Illumina MiSeq reads from 105 S. enterica 16S rRNA genes to the EnteroDB. The S. enterica non-exclusive plot (green) represents the percentage of hits to Salmonella and other Enterobacteriaceae. The S. enterica diagnostic plot (purple) represents the percentage of hits exclusive to Salmonella (left axis). The false negative rate plot (blue) represents the percentage of 16S rRNA fragments without a Salmonella best alignment (right axis)

    Techniques Used: Diagnostic Assay

    32) Product Images from "Molecular Subtyping of Treponema pallidum during a Local Syphilis Epidemic in Men Who Have Sex with Men in Melbourne, Australia"

    Article Title: Molecular Subtyping of Treponema pallidum during a Local Syphilis Epidemic in Men Who Have Sex with Men in Melbourne, Australia

    Journal: Journal of Clinical Microbiology

    doi: 10.1128/JCM.00083-12

    (A and B) Examples of PCR amplicons of the arp gene region showing different sizes. (A) Lanes 1 and 16, 100-bp DNA ladder; lanes 2 and 15, 1-kb DNA ladder; lanes 5, 6, 7, 9, 12, and 14, 14 repeats; lane 13, 12 repeats; lanes 3, 4, 8, 10, 11, and 16, product
    Figure Legend Snippet: (A and B) Examples of PCR amplicons of the arp gene region showing different sizes. (A) Lanes 1 and 16, 100-bp DNA ladder; lanes 2 and 15, 1-kb DNA ladder; lanes 5, 6, 7, 9, 12, and 14, 14 repeats; lane 13, 12 repeats; lanes 3, 4, 8, 10, 11, and 16, product

    Techniques Used: Polymerase Chain Reaction

    33) Product Images from "High-Throughput 3D Screening Reveals Differences in Drug Sensitivities between Culture Models of JIMT1 Breast Cancer Cells"

    Article Title: High-Throughput 3D Screening Reveals Differences in Drug Sensitivities between Culture Models of JIMT1 Breast Cancer Cells

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0077232

    Interferon pathway is activated in polyHEMA cultures. A . The canonical pathway that changed the most in PH4d and in PH7d compared to 2D according to IPA; the interferon pathway with arrows pointing to the top five changing genes in PH4d is shown in Table 2. Genes in red were upregulated in PH4d. Two hundred of the most up- and downregulated genes in PH4d/PH7d compared to the 2D cultures were subjected to IPA analysis. B . The gene expression results were validated by measuring interferon-alpha and beta activity from JIMT1 cells by transfecting them with a Cignal ISRE Reporter dual-luciferase assay kit (Qiagen). The kit measures induction of the STAT1 and STAT2 components of the JAK/STAT-signal transduction pathways as a readout for interferon activity. The cells were grown in 2D, MG, or PH for 3 days before reporter plasmids and transfection reagents were added for 24 hours. *** p-value
    Figure Legend Snippet: Interferon pathway is activated in polyHEMA cultures. A . The canonical pathway that changed the most in PH4d and in PH7d compared to 2D according to IPA; the interferon pathway with arrows pointing to the top five changing genes in PH4d is shown in Table 2. Genes in red were upregulated in PH4d. Two hundred of the most up- and downregulated genes in PH4d/PH7d compared to the 2D cultures were subjected to IPA analysis. B . The gene expression results were validated by measuring interferon-alpha and beta activity from JIMT1 cells by transfecting them with a Cignal ISRE Reporter dual-luciferase assay kit (Qiagen). The kit measures induction of the STAT1 and STAT2 components of the JAK/STAT-signal transduction pathways as a readout for interferon activity. The cells were grown in 2D, MG, or PH for 3 days before reporter plasmids and transfection reagents were added for 24 hours. *** p-value

    Techniques Used: Indirect Immunoperoxidase Assay, Expressing, Activity Assay, Luciferase, Transduction, Transfection

    34) Product Images from "Relevance of Foxp3+ regulatory T cells for early and late phases of murine sepsis"

    Article Title: Relevance of Foxp3+ regulatory T cells for early and late phases of murine sepsis

    Journal: Immunology

    doi: 10.1111/imm.12490

    DNA-methylation of CD4 + CD25 + Foxp3 + regulatory T (Treg) cells and CD4 + CD25 − T cells within the foxp3 Treg-specific demethylated region. (a) Schematic view of foxp3 locus illustrates the intron–exon (rectangles) structure, including the foxp3 Treg-specific demethylated region (TSDR). Enlargements of 12 CpGs of the foxp3-TSDR are shown. Results of next-generation amplicon sequencing show the degree (%) of methylation of each of the 12 CpGs in CD4 + CD25 − T cells (red) and CD4 + CD25 + Foxp3 + T cells (blue). The three CpGs, spanned by the TaqMan probes of a quantitative analysis of methylated alleles (QAMA) assay, are framed. (b) Results of QAMA assay in Foxp3 + Treg cells and CD4 + CD25 − T cells of splenocytes from naive and septic mice 4 days after caecal ligation and puncture (CLP) displays the degree of methylation within the foxp3-TSDR ( n = 4 to n
    Figure Legend Snippet: DNA-methylation of CD4 + CD25 + Foxp3 + regulatory T (Treg) cells and CD4 + CD25 − T cells within the foxp3 Treg-specific demethylated region. (a) Schematic view of foxp3 locus illustrates the intron–exon (rectangles) structure, including the foxp3 Treg-specific demethylated region (TSDR). Enlargements of 12 CpGs of the foxp3-TSDR are shown. Results of next-generation amplicon sequencing show the degree (%) of methylation of each of the 12 CpGs in CD4 + CD25 − T cells (red) and CD4 + CD25 + Foxp3 + T cells (blue). The three CpGs, spanned by the TaqMan probes of a quantitative analysis of methylated alleles (QAMA) assay, are framed. (b) Results of QAMA assay in Foxp3 + Treg cells and CD4 + CD25 − T cells of splenocytes from naive and septic mice 4 days after caecal ligation and puncture (CLP) displays the degree of methylation within the foxp3-TSDR ( n = 4 to n

    Techniques Used: DNA Methylation Assay, Amplification, Sequencing, Methylation, Mouse Assay, Ligation

    35) Product Images from "Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps"

    Article Title: Microbial characterization of bee pollen from the Vesuvius area collected by using three different traps

    Journal: PLoS ONE

    doi: 10.1371/journal.pone.0183208

    Relative abundance of OUT’s based on 16S rRNA gene by pyrosequencing analysis of DNA from pollen samples.
    Figure Legend Snippet: Relative abundance of OUT’s based on 16S rRNA gene by pyrosequencing analysis of DNA from pollen samples.

    Techniques Used:

    36) Product Images from "Next generation sequencing and comparative analyses of Xenopus mitogenomes"

    Article Title: Next generation sequencing and comparative analyses of Xenopus mitogenomes

    Journal: BMC Genomics

    doi: 10.1186/1471-2164-13-496

    Xenopus borealis mitochondrial genome. The complete mitochondrial genome of Xenopus borealis (17,474 bp, drawn to scale) All 13 protein coding genes are shown as open arrows, 2 ribosomal RNAs as shaded arrows and 22 tRNAs as arrowed lines. Each tRNA is shown by its single letter amino acid code. The two leucine and two serine tRNAs are differentiated by their respective anti-codons. The direction of transcription is indicated by the arrows. Also shown is the non-coding D-loop (control region, black) and the position of the primers (LongF1/R2 and LongF2/R1) used to generate the two long-PCR amplicons, which were pooled and sequenced using 454 technology.
    Figure Legend Snippet: Xenopus borealis mitochondrial genome. The complete mitochondrial genome of Xenopus borealis (17,474 bp, drawn to scale) All 13 protein coding genes are shown as open arrows, 2 ribosomal RNAs as shaded arrows and 22 tRNAs as arrowed lines. Each tRNA is shown by its single letter amino acid code. The two leucine and two serine tRNAs are differentiated by their respective anti-codons. The direction of transcription is indicated by the arrows. Also shown is the non-coding D-loop (control region, black) and the position of the primers (LongF1/R2 and LongF2/R1) used to generate the two long-PCR amplicons, which were pooled and sequenced using 454 technology.

    Techniques Used: Polymerase Chain Reaction

    Long PCR, COX1, 16S, primer region 1 and primer region 2 amplicons. Agarose gel electrophoresis of ( A ) Xenopus borealis (XB; lanes 1 and 2) and X. victorianus (XV; lanes 3 and 4) PCR fragments using Long F1/R2 (lanes 1 and 3) and Long F2/R1 primers (lanes 2 and 4). ( B ) XB (lanes 1 and 2) and XV (lane 3) PCR fragments using COX1 (lane 1) and 16SA-Lmod/H (lanes 2 and 3) primers. ( C ) XB (lanes 1-2 and 5-6) and XV (lanes 3-4 and 7-8) PCR fragments using AMP1F/R (lanes 1-4) and AMP2F/R (lanes 5-8) primers. M1 and M2 = 1kb and 100bp DNA ladders, respectively.
    Figure Legend Snippet: Long PCR, COX1, 16S, primer region 1 and primer region 2 amplicons. Agarose gel electrophoresis of ( A ) Xenopus borealis (XB; lanes 1 and 2) and X. victorianus (XV; lanes 3 and 4) PCR fragments using Long F1/R2 (lanes 1 and 3) and Long F2/R1 primers (lanes 2 and 4). ( B ) XB (lanes 1 and 2) and XV (lane 3) PCR fragments using COX1 (lane 1) and 16SA-Lmod/H (lanes 2 and 3) primers. ( C ) XB (lanes 1-2 and 5-6) and XV (lanes 3-4 and 7-8) PCR fragments using AMP1F/R (lanes 1-4) and AMP2F/R (lanes 5-8) primers. M1 and M2 = 1kb and 100bp DNA ladders, respectively.

    Techniques Used: Polymerase Chain Reaction, Agarose Gel Electrophoresis

    37) Product Images from "HIV-1 Drug Resistance in the iPrEx Preexposure Prophylaxis Trial"

    Article Title: HIV-1 Drug Resistance in the iPrEx Preexposure Prophylaxis Trial

    Journal: The Journal of Infectious Diseases

    doi: 10.1093/infdis/jiu233

    Schematic of the qMVA for low-level drug resistance. A , FTC/TDF selected mutations measured by the qMVA. DNA amplicons spanning TDF-associated mutations K65R, K70E, and FTC-associated mutations M184V/I are generated by nested RT-PCR from plasma HIV-1 virions, representing the predominant and minor quasispecies. The example shows a hypothetical viral mixture at rt 65 with 99% WT (consensus B codon AAA, Lys) and 1.0% Mut (consensus B codon AGA, Arg) where the mutant sequence is undetectable by population sequencing. B , Cure PCR step. The cure PCR step is performed prior to the AS-PCR step to normalize possible sequence heterogeneity in the AS-PCR primer target sites that can reduce PCR efficiency and result in inaccurate quantification of the minor variant population. The example portrays a virus that differs from the discriminatory AS-PCR primer at 2 sites upstream from the SNP conferring resistance. A low-stringency PCR with limited cycle number is performed on the mixed WT (99%) and Mut (1%) DNA amplicons, using a consensus sequence-based primer pair covering the AS-PCR target sites adjacent to but not including the SNP conferring resistance. When paired with another consensus primer, AS-PCR target amplicons are generated representing the original WT:Mut SNP mixtures, but with AS-PCR target sequences normalized to HIV-1 consensus sequences. C , AS-PCR reaction. Amplicons generated by the cure PCR are diluted appropriately and duplicate PCR reactions are performed with primers specific for the WT or Mut SNP. The discriminatory capability of the AS-PCR primers is enhanced by incorporating a 3′, -2 base mismatch into the AS-PCR primer [ 36 ]. D , Determining percent mutant by ΔCt. The percent minor variant in a mixture of WT:Mut amplicons is determined by ΔCt measurements from real-time PCR using WT- and Mut-specific discriminatory primers. When extrapolated by linear regression against a 6-point standard curve run simultaneously (0.1% to 24.3% Mut input in WT background), the percent minor variant (65R) can be derived. Abbreviations: AS-PCR, allele-specific polymerase chain reaction; FTC, emtricitabine; HIV, human immunodeficiency virus; Mut, mutant; PCR, polymerase chain reaction; qMVA, quantitative minor variant assay; RT-PCR, reverse-transcriptase PCR; SNP, single nucleotide polymorphism; TDF, tenofovir disoproxil fumarate; WT, wild-type.
    Figure Legend Snippet: Schematic of the qMVA for low-level drug resistance. A , FTC/TDF selected mutations measured by the qMVA. DNA amplicons spanning TDF-associated mutations K65R, K70E, and FTC-associated mutations M184V/I are generated by nested RT-PCR from plasma HIV-1 virions, representing the predominant and minor quasispecies. The example shows a hypothetical viral mixture at rt 65 with 99% WT (consensus B codon AAA, Lys) and 1.0% Mut (consensus B codon AGA, Arg) where the mutant sequence is undetectable by population sequencing. B , Cure PCR step. The cure PCR step is performed prior to the AS-PCR step to normalize possible sequence heterogeneity in the AS-PCR primer target sites that can reduce PCR efficiency and result in inaccurate quantification of the minor variant population. The example portrays a virus that differs from the discriminatory AS-PCR primer at 2 sites upstream from the SNP conferring resistance. A low-stringency PCR with limited cycle number is performed on the mixed WT (99%) and Mut (1%) DNA amplicons, using a consensus sequence-based primer pair covering the AS-PCR target sites adjacent to but not including the SNP conferring resistance. When paired with another consensus primer, AS-PCR target amplicons are generated representing the original WT:Mut SNP mixtures, but with AS-PCR target sequences normalized to HIV-1 consensus sequences. C , AS-PCR reaction. Amplicons generated by the cure PCR are diluted appropriately and duplicate PCR reactions are performed with primers specific for the WT or Mut SNP. The discriminatory capability of the AS-PCR primers is enhanced by incorporating a 3′, -2 base mismatch into the AS-PCR primer [ 36 ]. D , Determining percent mutant by ΔCt. The percent minor variant in a mixture of WT:Mut amplicons is determined by ΔCt measurements from real-time PCR using WT- and Mut-specific discriminatory primers. When extrapolated by linear regression against a 6-point standard curve run simultaneously (0.1% to 24.3% Mut input in WT background), the percent minor variant (65R) can be derived. Abbreviations: AS-PCR, allele-specific polymerase chain reaction; FTC, emtricitabine; HIV, human immunodeficiency virus; Mut, mutant; PCR, polymerase chain reaction; qMVA, quantitative minor variant assay; RT-PCR, reverse-transcriptase PCR; SNP, single nucleotide polymorphism; TDF, tenofovir disoproxil fumarate; WT, wild-type.

    Techniques Used: Generated, Reverse Transcription Polymerase Chain Reaction, Mutagenesis, Sequencing, Polymerase Chain Reaction, Variant Assay, Real-time Polymerase Chain Reaction, Derivative Assay

    38) Product Images from "8-Bromo-cyclic inosine diphosphoribose: towards a selective cyclic ADP-ribose agonist"

    Article Title: 8-Bromo-cyclic inosine diphosphoribose: towards a selective cyclic ADP-ribose agonist

    Journal: Biochemical Journal

    doi: 10.1042/BJ20082308

    Effect of 8-Br- N 1 -cIDPR on Ca 2+ signalling in HEK293 cells overexpressing TRPM2 HEK-293 cells transfected with ( a )–( c ) pIRES2-EGFP-TRPM2 (TRPM2) and ( d )–( f ) pIRES2-EGFP (EGFP control) were loaded with Fura-2AM and subjected to Ca 2+ imaging. Time points of addition of a maximal concentration of ( a and d ) 100 or 300 μM H 2 O 2 , ( b ) and ( e ) 1 mM 8-Br- N 1 -cIDPR, or ( c ) and ( f ) buffer are indicated. Characteristic tracings of a representative experiment are shown. ( g ) Concentration–response curve of 8-Br- N 1 -cIDPR in transfected HEK-293 cells ( n =6–67) represented as means±S.E.M. of single tracings from time points 100–600 s (the Ca 2+ peak).
    Figure Legend Snippet: Effect of 8-Br- N 1 -cIDPR on Ca 2+ signalling in HEK293 cells overexpressing TRPM2 HEK-293 cells transfected with ( a )–( c ) pIRES2-EGFP-TRPM2 (TRPM2) and ( d )–( f ) pIRES2-EGFP (EGFP control) were loaded with Fura-2AM and subjected to Ca 2+ imaging. Time points of addition of a maximal concentration of ( a and d ) 100 or 300 μM H 2 O 2 , ( b ) and ( e ) 1 mM 8-Br- N 1 -cIDPR, or ( c ) and ( f ) buffer are indicated. Characteristic tracings of a representative experiment are shown. ( g ) Concentration–response curve of 8-Br- N 1 -cIDPR in transfected HEK-293 cells ( n =6–67) represented as means±S.E.M. of single tracings from time points 100–600 s (the Ca 2+ peak).

    Techniques Used: Transfection, Imaging, Concentration Assay

    Activation of endogenous TRPM2 currents in Jurkat T-cells by infusion of ADPR, cADPR and 8-Br- N 1 -cIDPR All experiments were carried out with 2 mM extracellular Ca 2+ and with unbuffered intracellular Ca 2+ as described in [ 35 ]. Voltage ramps from −85 mV to +65 mV were applied every 5 s. ( a ) Representative membrane current over time recorded at −80 mV induced by perfusion with 300 μM ADPR. ( b ) Representative current–voltage relationship derived from currents evoked by voltage ramps from −85 mV to +65 mV. ( c ) Concentration–response relationship for activation of TRPM2 currents by infusion of ADPR (○, n =6–8), cADPR (▵, n =5–8) and 300 μM 8-Br- N 1 -cIDPR (●, n =6). Results represent means±S.E.M. of maximum current at −80 mV. ( d ) TRPM2 currents at −80 mV after infusion of 30 μM ADPR ( n =8), co-infusion of 5 μM cADPR and 30 μM ADPR ( n =9), 100 μM cADPR and 30 μM ADPR ( n =8), and 300 μM 8-Br- N1 -cIDPR and 30 μM ADPR ( n =6). Results represent means± S.E.M of maximum current at −80 mV. ( e ) RP-HPLC analysis of cADPR used in the infusion experiments.
    Figure Legend Snippet: Activation of endogenous TRPM2 currents in Jurkat T-cells by infusion of ADPR, cADPR and 8-Br- N 1 -cIDPR All experiments were carried out with 2 mM extracellular Ca 2+ and with unbuffered intracellular Ca 2+ as described in [ 35 ]. Voltage ramps from −85 mV to +65 mV were applied every 5 s. ( a ) Representative membrane current over time recorded at −80 mV induced by perfusion with 300 μM ADPR. ( b ) Representative current–voltage relationship derived from currents evoked by voltage ramps from −85 mV to +65 mV. ( c ) Concentration–response relationship for activation of TRPM2 currents by infusion of ADPR (○, n =6–8), cADPR (▵, n =5–8) and 300 μM 8-Br- N 1 -cIDPR (●, n =6). Results represent means±S.E.M. of maximum current at −80 mV. ( d ) TRPM2 currents at −80 mV after infusion of 30 μM ADPR ( n =8), co-infusion of 5 μM cADPR and 30 μM ADPR ( n =9), 100 μM cADPR and 30 μM ADPR ( n =8), and 300 μM 8-Br- N1 -cIDPR and 30 μM ADPR ( n =6). Results represent means± S.E.M of maximum current at −80 mV. ( e ) RP-HPLC analysis of cADPR used in the infusion experiments.

    Techniques Used: Activation Assay, Derivative Assay, Concentration Assay, High Performance Liquid Chromatography

    39) Product Images from "From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children"

    Article Title: From an imbalance to a new imbalance: Italian-style gluten-free diet alters the salivary microbiota and metabolome of African celiac children

    Journal: Scientific Reports

    doi: 10.1038/srep18571

    Principle Coordinate Analysis (PCoA). The analysis was based on unweighted UniFrac distance matrix of all 16S rRNA gene sequences found on salivary samples of Saharawi celiac children under African-style gluten-free (T0), and after 30 (T30) and 60 (T60) days of intervention with Italian-style gluten-free diet.
    Figure Legend Snippet: Principle Coordinate Analysis (PCoA). The analysis was based on unweighted UniFrac distance matrix of all 16S rRNA gene sequences found on salivary samples of Saharawi celiac children under African-style gluten-free (T0), and after 30 (T30) and 60 (T60) days of intervention with Italian-style gluten-free diet.

    Techniques Used:

    40) Product Images from "Direct Detection by In Situ PCR of the amoA Gene in Biofilm Resulting from a Nitrogen Removal Process"

    Article Title: Direct Detection by In Situ PCR of the amoA Gene in Biofilm Resulting from a Nitrogen Removal Process

    Journal: Applied and Environmental Microbiology

    doi: 10.1128/AEM.67.11.5261-5266.2001

    Detection of the cells possessing amoA in pure culture (A) and in the biofilm (B and C), with Alexa Fluor 488-labeled antidigoxigenin antibody. Panels B and C show the same biofilm. The yellow color indicates positive cells, while the red shows negative cells. The portion of panel B that was magnified to produce panel C is indicated with a white box.
    Figure Legend Snippet: Detection of the cells possessing amoA in pure culture (A) and in the biofilm (B and C), with Alexa Fluor 488-labeled antidigoxigenin antibody. Panels B and C show the same biofilm. The yellow color indicates positive cells, while the red shows negative cells. The portion of panel B that was magnified to produce panel C is indicated with a white box.

    Techniques Used: Labeling

    Detection of ammonia-oxidizing bacterial cells possessing amoA gene in pure culture (A) and in the biofilm (B and C), with alkaline phosphatase-labeled antidigoxigenin antibody. Panels B and C show the same biofilm. The yellow color indicates positive cells, while the green shows negative cells (arrows indicate the nonspecific signal). The portion of panel B that was magnified to produce panel C is indicated with a white box.
    Figure Legend Snippet: Detection of ammonia-oxidizing bacterial cells possessing amoA gene in pure culture (A) and in the biofilm (B and C), with alkaline phosphatase-labeled antidigoxigenin antibody. Panels B and C show the same biofilm. The yellow color indicates positive cells, while the green shows negative cells (arrows indicate the nonspecific signal). The portion of panel B that was magnified to produce panel C is indicated with a white box.

    Techniques Used: Labeling

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    Article Title: Hepatitis B Viral DNA Decline at Loss of HBeAg Is Mainly Explained by Reduced cccDNA Load - Down-Regulated Transcription of PgRNA Has Limited Impact
    Article Snippet: .. Extraction of DNA and RNA from Cells DNA and RNA were extracted from transfected and non-transfected hepatoma cells in a Magnapure robot (Roche Applied Science, Germany) using the Total NA protocol. .. Harvested cells were washed in 1 mL PBS and after centrifugation at 5000 rpm for 3 min the pellet was re-suspended in 800 µL RLT lysis buffer (Qiagen Sciences, MD, USA) before extraction.

    Synthesized:

    Article Title: Chronic hypoxia‐induced slug promotes invasive behavior of prostate cancer cells by activating expression of ephrin‐B1, et al. Chronic hypoxia‐induced slug promotes invasive behavior of prostate cancer cells by activating expression of ephrin‐B1
    Article Snippet: .. 2.5 Real‐time quantitative RT‐PCR First‐strand cDNA was synthesized from the total RNA using ThermoScript RT‐PCR System (Roche, Indianapolis, IN, USA). .. PCR was performed on a LightCycler system (Roche) using LightCycler FastStart DNA Master SYBR Green I reaction mix (Roche) and QuantiTect Primer Assays (QIAGEN, Hilden, Germany).

    Isolation:

    Article Title: MERS-coronavirus replication induces severe in vitro cytopathology and is strongly inhibited by cyclosporin A or interferon-? treatment
    Article Snippet: .. RNA from 200 µl culture medium of CoV-infected cells was isolated with a MagnaPure LC Total Nucleic Acid Isolation kit (Roche) and eluted in 100 µl. .. RT-PCR conditions for quantifying MERS-CoV and SARS-CoV RNA and amplification parameters have been described previously ( ; ).

    Article Title: Homologous Recombination Occurs in Entamoeba and Is Enhanced during Growth Stress and Stage Conversion
    Article Snippet: .. RNA purification and Real Time RT-PCR Entamoeba cells were harvested and suspended immediately in TriZol reagent (Invitrogen) and RNA was isolated and treated with DNase I (Roche) according to manufacturer's protocol. .. RNA was reverse transcribed into cDNA using Superscript III reverse transcriptase (Invitrogen) and random hexamers used as a primer.

    Article Title: Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
    Article Snippet: .. Reverse transcription quantitative PCR (RT-qPCR) Total RNA was isolated from two million cells by SV total RNA isolation kit (Promega). cDNA was prepared by annealing 500 ng RNA with oligo dT as per the manufacturer’s instructions (Transcriptor High Fidelity cDNA Synthesis kit, Roche). ..

    Quantitative RT-PCR:

    Article Title: Chronic hypoxia‐induced slug promotes invasive behavior of prostate cancer cells by activating expression of ephrin‐B1, et al. Chronic hypoxia‐induced slug promotes invasive behavior of prostate cancer cells by activating expression of ephrin‐B1
    Article Snippet: .. 2.5 Real‐time quantitative RT‐PCR First‐strand cDNA was synthesized from the total RNA using ThermoScript RT‐PCR System (Roche, Indianapolis, IN, USA). .. PCR was performed on a LightCycler system (Roche) using LightCycler FastStart DNA Master SYBR Green I reaction mix (Roche) and QuantiTect Primer Assays (QIAGEN, Hilden, Germany).

    Article Title: Homologous Recombination Occurs in Entamoeba and Is Enhanced during Growth Stress and Stage Conversion
    Article Snippet: .. RNA purification and Real Time RT-PCR Entamoeba cells were harvested and suspended immediately in TriZol reagent (Invitrogen) and RNA was isolated and treated with DNase I (Roche) according to manufacturer's protocol. .. RNA was reverse transcribed into cDNA using Superscript III reverse transcriptase (Invitrogen) and random hexamers used as a primer.

    Article Title: Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
    Article Snippet: .. Reverse transcription quantitative PCR (RT-qPCR) Total RNA was isolated from two million cells by SV total RNA isolation kit (Promega). cDNA was prepared by annealing 500 ng RNA with oligo dT as per the manufacturer’s instructions (Transcriptor High Fidelity cDNA Synthesis kit, Roche). ..

    Purification:

    Article Title: Homologous Recombination Occurs in Entamoeba and Is Enhanced during Growth Stress and Stage Conversion
    Article Snippet: .. RNA purification and Real Time RT-PCR Entamoeba cells were harvested and suspended immediately in TriZol reagent (Invitrogen) and RNA was isolated and treated with DNase I (Roche) according to manufacturer's protocol. .. RNA was reverse transcribed into cDNA using Superscript III reverse transcriptase (Invitrogen) and random hexamers used as a primer.

    Real-time Polymerase Chain Reaction:

    Article Title: Genome-wide analyses reveal the IRE1a-XBP1 pathway promotes T helper cell differentiation by resolving secretory stress and accelerating proliferation
    Article Snippet: .. Reverse transcription quantitative PCR (RT-qPCR) Total RNA was isolated from two million cells by SV total RNA isolation kit (Promega). cDNA was prepared by annealing 500 ng RNA with oligo dT as per the manufacturer’s instructions (Transcriptor High Fidelity cDNA Synthesis kit, Roche). ..

    Reverse Transcription Polymerase Chain Reaction:

    Article Title: Chronic hypoxia‐induced slug promotes invasive behavior of prostate cancer cells by activating expression of ephrin‐B1, et al. Chronic hypoxia‐induced slug promotes invasive behavior of prostate cancer cells by activating expression of ephrin‐B1
    Article Snippet: .. 2.5 Real‐time quantitative RT‐PCR First‐strand cDNA was synthesized from the total RNA using ThermoScript RT‐PCR System (Roche, Indianapolis, IN, USA). .. PCR was performed on a LightCycler system (Roche) using LightCycler FastStart DNA Master SYBR Green I reaction mix (Roche) and QuantiTect Primer Assays (QIAGEN, Hilden, Germany).

    Article Title: Arabidopsis ETO1 specifically interacts with and negatively regulates type 2 1-aminocyclopropane-1-carboxylate synthases
    Article Snippet: .. RNA (1 μg) was used in each RT-PCR following the manufacturer's protocol (Titan One Tube RT-PCR System, Roche Diagnostics). ..

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  • 85
    Roche amplicor hbv monitor kit
    Log-log 10 graph showing the linear regression comparing VL data obtained from 47 matched samples of DBS vs. Plasma . Log 10 measurements of the <t>HBV</t> DNA in DBS and Plasma samples, assessed by Cobas Monitor <t>Amplicor.</t> The values for the DBS are plotted against the values for the matched plasma samples. The linear correlation between the two samples is shown (R 2 = 0.86). The Pearson correlation coefficient was 0.93.
    Amplicor Hbv Monitor Kit, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Average 85 stars, based on 1 article reviews
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    amplicor hbv monitor kit - by Bioz Stars, 2020-09
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    91
    Roche cobas amplicor system v1 5 kit
    HIV-1 infection affects human cell distributions in dual blood and brain humanized mice. (A) Examples showing CD4 + cell decline in the peripheral blood of HIV-1-infected mice, with a relative increase in the CD8 + cell compartment. (B) Quantification of human CD4 and CD8T cells in the peripheral blood of infected ( n =6) and control ( n =6) mice. Multiple t -tests using the Holm–Sidak method for multiple comparisons correction were applied to examine significant differences between groups. Data are mean±s.e.m. *Adjusted P =0.045. (C) Immunohistology of spleen sections shows HLA-DR + cells and the presence of HIV-1-infected cells stained for HIV-1 p24. Images were captured by a Nuance multiplex system at an original magnification of 200×. Scale bar: 100 μm. (D) Peripheral viral load was determined by a <t>COBAS</t> <t>Amplicor</t> System. Each symbol represents an individual infected mouse from all experiments. (E) Viral RNA levels were determined by semi-nested RT-PCR in the HIV + group ( n =3, red) and the control group ( n =3, blue) in two brain regions, FC and STR. (F) Immunohistology of brain sections showing the presence of activated HLA-DR + cells and HIV-1 p24 + -infected cells on adjacent serial section. Representative images from the meningeal space containing vascular vessels are shown. Images were captured by a Nuance multiplex system at an original magnification of 200×. Insets show cells at a magnification of 1000×. Scale bars: 100 μm (20 μm in inset). (G) Quantification of infiltrating HLA-DR + and CD163 + cells in the brain regions of HIV-1-infected ( n =5) and uninfected dual reconstituted mice ( n =6). Two-way ANOVA using Sidak's multiple comparisons correction was used to examine significant differences between groups. Data are mean±s.e.m. * P =0.017, **** P
    Cobas Amplicor System V1 5 Kit, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 2 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/result/cobas amplicor system v1 5 kit/product/Roche
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    85
    Roche amplicor ct ng kit
    The prevalence of Chlamydia trachomatis infection* in children aged 1 to 9 years for the 14 villages † . Individual villages are represented by the grey lines. Several villages overlie each other with a prevalence of 0%. The overall village level average is represented by the black line. * Chlamydia trachomatis infection determined by <t>Amplicor</t> CT PCR assay. † Village No. 12 withdrew after 17-months.
    Amplicor Ct Ng Kit, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 5 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    85
    Roche cobas amplicor hbv monitor kits
    Deming regression comparison of samples run undiluted and diluted in the <t>COBAS</t> <t>Amplicor</t> <t>HBV</t> Monitor assay (Amplicor). Forty-one clinical samples tested undiluted and diluted in the Amplicor assay are shown. Deming regression comparing undiluted and diluted
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    Image Search Results


    Log-log 10 graph showing the linear regression comparing VL data obtained from 47 matched samples of DBS vs. Plasma . Log 10 measurements of the HBV DNA in DBS and Plasma samples, assessed by Cobas Monitor Amplicor. The values for the DBS are plotted against the values for the matched plasma samples. The linear correlation between the two samples is shown (R 2 = 0.86). The Pearson correlation coefficient was 0.93.

    Journal: Virology Journal

    Article Title: Use of dried blood samples for monitoring hepatitis B virus infection

    doi: 10.1186/1743-422X-6-153

    Figure Lengend Snippet: Log-log 10 graph showing the linear regression comparing VL data obtained from 47 matched samples of DBS vs. Plasma . Log 10 measurements of the HBV DNA in DBS and Plasma samples, assessed by Cobas Monitor Amplicor. The values for the DBS are plotted against the values for the matched plasma samples. The linear correlation between the two samples is shown (R 2 = 0.86). The Pearson correlation coefficient was 0.93.

    Article Snippet: c) Plasma viral load (VL) quantification The levels of HBV DNA in 100 μl of plasma were quantified by using the Amplicor HBV Monitor kit (Roche Molecular Systems, Inc.) according to the manufacturer's instructions.

    Techniques:

    HIV-1 infection affects human cell distributions in dual blood and brain humanized mice. (A) Examples showing CD4 + cell decline in the peripheral blood of HIV-1-infected mice, with a relative increase in the CD8 + cell compartment. (B) Quantification of human CD4 and CD8T cells in the peripheral blood of infected ( n =6) and control ( n =6) mice. Multiple t -tests using the Holm–Sidak method for multiple comparisons correction were applied to examine significant differences between groups. Data are mean±s.e.m. *Adjusted P =0.045. (C) Immunohistology of spleen sections shows HLA-DR + cells and the presence of HIV-1-infected cells stained for HIV-1 p24. Images were captured by a Nuance multiplex system at an original magnification of 200×. Scale bar: 100 μm. (D) Peripheral viral load was determined by a COBAS Amplicor System. Each symbol represents an individual infected mouse from all experiments. (E) Viral RNA levels were determined by semi-nested RT-PCR in the HIV + group ( n =3, red) and the control group ( n =3, blue) in two brain regions, FC and STR. (F) Immunohistology of brain sections showing the presence of activated HLA-DR + cells and HIV-1 p24 + -infected cells on adjacent serial section. Representative images from the meningeal space containing vascular vessels are shown. Images were captured by a Nuance multiplex system at an original magnification of 200×. Insets show cells at a magnification of 1000×. Scale bars: 100 μm (20 μm in inset). (G) Quantification of infiltrating HLA-DR + and CD163 + cells in the brain regions of HIV-1-infected ( n =5) and uninfected dual reconstituted mice ( n =6). Two-way ANOVA using Sidak's multiple comparisons correction was used to examine significant differences between groups. Data are mean±s.e.m. * P =0.017, **** P

    Journal: Disease Models & Mechanisms

    Article Title: Systemic HIV-1 infection produces a unique glial footprint in humanized mouse brains

    doi: 10.1242/dmm.031773

    Figure Lengend Snippet: HIV-1 infection affects human cell distributions in dual blood and brain humanized mice. (A) Examples showing CD4 + cell decline in the peripheral blood of HIV-1-infected mice, with a relative increase in the CD8 + cell compartment. (B) Quantification of human CD4 and CD8T cells in the peripheral blood of infected ( n =6) and control ( n =6) mice. Multiple t -tests using the Holm–Sidak method for multiple comparisons correction were applied to examine significant differences between groups. Data are mean±s.e.m. *Adjusted P =0.045. (C) Immunohistology of spleen sections shows HLA-DR + cells and the presence of HIV-1-infected cells stained for HIV-1 p24. Images were captured by a Nuance multiplex system at an original magnification of 200×. Scale bar: 100 μm. (D) Peripheral viral load was determined by a COBAS Amplicor System. Each symbol represents an individual infected mouse from all experiments. (E) Viral RNA levels were determined by semi-nested RT-PCR in the HIV + group ( n =3, red) and the control group ( n =3, blue) in two brain regions, FC and STR. (F) Immunohistology of brain sections showing the presence of activated HLA-DR + cells and HIV-1 p24 + -infected cells on adjacent serial section. Representative images from the meningeal space containing vascular vessels are shown. Images were captured by a Nuance multiplex system at an original magnification of 200×. Insets show cells at a magnification of 1000×. Scale bars: 100 μm (20 μm in inset). (G) Quantification of infiltrating HLA-DR + and CD163 + cells in the brain regions of HIV-1-infected ( n =5) and uninfected dual reconstituted mice ( n =6). Two-way ANOVA using Sidak's multiple comparisons correction was used to examine significant differences between groups. Data are mean±s.e.m. * P =0.017, **** P

    Article Snippet: Measurements of viral load in plasma and brain tissues Viral RNA copies in the murine plasma were determined by using a COBAS Amplicor System v1.5 kit (Roche Molecular Diagnostics, Pleasanton, CA, USA).

    Techniques: Infection, Mouse Assay, Staining, Multiplex Assay, Reverse Transcription Polymerase Chain Reaction

    The prevalence of Chlamydia trachomatis infection* in children aged 1 to 9 years for the 14 villages † . Individual villages are represented by the grey lines. Several villages overlie each other with a prevalence of 0%. The overall village level average is represented by the black line. * Chlamydia trachomatis infection determined by Amplicor CT PCR assay. † Village No. 12 withdrew after 17-months.

    Journal: PLoS Neglected Tropical Diseases

    Article Title: Profound and Sustained Reduction in Chlamydia trachomatis in The Gambia: A Five-Year Longitudinal Study of Trachoma Endemic Communities

    doi: 10.1371/journal.pntd.0000835

    Figure Lengend Snippet: The prevalence of Chlamydia trachomatis infection* in children aged 1 to 9 years for the 14 villages † . Individual villages are represented by the grey lines. Several villages overlie each other with a prevalence of 0%. The overall village level average is represented by the black line. * Chlamydia trachomatis infection determined by Amplicor CT PCR assay. † Village No. 12 withdrew after 17-months.

    Article Snippet: Detection of C. trachomatis C. trachomatis was detected using the Amplicor CT/NG kit (Roche Molecular Systems, Branchburg, NJ).

    Techniques: Infection, Polymerase Chain Reaction

    Deming regression comparison of samples run undiluted and diluted in the COBAS Amplicor HBV Monitor assay (Amplicor). Forty-one clinical samples tested undiluted and diluted in the Amplicor assay are shown. Deming regression comparing undiluted and diluted

    Journal: Journal of Clinical Microbiology

    Article Title: Evaluation of the COBAS Amplicor HBV Monitor Assay and Comparison with the Ultrasensitive HBV Hybrid Capture 2 Assay for Quantification of Hepatitis B Virus DNA

    doi: 10.1128/JCM.43.2.596-603.2005

    Figure Lengend Snippet: Deming regression comparison of samples run undiluted and diluted in the COBAS Amplicor HBV Monitor assay (Amplicor). Forty-one clinical samples tested undiluted and diluted in the Amplicor assay are shown. Deming regression comparing undiluted and diluted

    Article Snippet: COBAS Amplicor HBV Monitor kits were supplied by Roche Molecular Systems, Pleasanton, Calif.

    Techniques:

    Between-run precision of COBAS Amplicor HBV Monitor assay. Fifty-two clinical samples were tested undiluted in duplicate in the Amplicor assay on separate days. The means and standard deviations of log HBV DNA copies/milliliter of the duplicate values

    Journal: Journal of Clinical Microbiology

    Article Title: Evaluation of the COBAS Amplicor HBV Monitor Assay and Comparison with the Ultrasensitive HBV Hybrid Capture 2 Assay for Quantification of Hepatitis B Virus DNA

    doi: 10.1128/JCM.43.2.596-603.2005

    Figure Lengend Snippet: Between-run precision of COBAS Amplicor HBV Monitor assay. Fifty-two clinical samples were tested undiluted in duplicate in the Amplicor assay on separate days. The means and standard deviations of log HBV DNA copies/milliliter of the duplicate values

    Article Snippet: COBAS Amplicor HBV Monitor kits were supplied by Roche Molecular Systems, Pleasanton, Calif.

    Techniques:

    Within-run precision of COBAS Amplicor HBV Monitor and Ultrasensitive Digene HC2 assays. Eight samples were serially diluted in HBV-seronegative NHS and tested in the Amplicor and HC2 assays in triplicate on the same day. The means and standard deviations

    Journal: Journal of Clinical Microbiology

    Article Title: Evaluation of the COBAS Amplicor HBV Monitor Assay and Comparison with the Ultrasensitive HBV Hybrid Capture 2 Assay for Quantification of Hepatitis B Virus DNA

    doi: 10.1128/JCM.43.2.596-603.2005

    Figure Lengend Snippet: Within-run precision of COBAS Amplicor HBV Monitor and Ultrasensitive Digene HC2 assays. Eight samples were serially diluted in HBV-seronegative NHS and tested in the Amplicor and HC2 assays in triplicate on the same day. The means and standard deviations

    Article Snippet: COBAS Amplicor HBV Monitor kits were supplied by Roche Molecular Systems, Pleasanton, Calif.

    Techniques:

    COBAS Amplicor HBV Monitor assay linearity. Eight samples were serially diluted in HBV-seronegative NHS and tested by the Amplicor assay in triplicate on the same day. The means of triplicate values were calculated and plotted as log HBV DNA copies/milliliter.

    Journal: Journal of Clinical Microbiology

    Article Title: Evaluation of the COBAS Amplicor HBV Monitor Assay and Comparison with the Ultrasensitive HBV Hybrid Capture 2 Assay for Quantification of Hepatitis B Virus DNA

    doi: 10.1128/JCM.43.2.596-603.2005

    Figure Lengend Snippet: COBAS Amplicor HBV Monitor assay linearity. Eight samples were serially diluted in HBV-seronegative NHS and tested by the Amplicor assay in triplicate on the same day. The means of triplicate values were calculated and plotted as log HBV DNA copies/milliliter.

    Article Snippet: COBAS Amplicor HBV Monitor kits were supplied by Roche Molecular Systems, Pleasanton, Calif.

    Techniques:

    Deming regression comparison of Digene HC2 assay and COBAS Amplicor HBV Monitor assay. One-hundred samples previously tested using the HC2 assay were tested undiluted in the Amplicor assay. Samples with results greater than 200,000 HBV DNA copies/ml were

    Journal: Journal of Clinical Microbiology

    Article Title: Evaluation of the COBAS Amplicor HBV Monitor Assay and Comparison with the Ultrasensitive HBV Hybrid Capture 2 Assay for Quantification of Hepatitis B Virus DNA

    doi: 10.1128/JCM.43.2.596-603.2005

    Figure Lengend Snippet: Deming regression comparison of Digene HC2 assay and COBAS Amplicor HBV Monitor assay. One-hundred samples previously tested using the HC2 assay were tested undiluted in the Amplicor assay. Samples with results greater than 200,000 HBV DNA copies/ml were

    Article Snippet: COBAS Amplicor HBV Monitor kits were supplied by Roche Molecular Systems, Pleasanton, Calif.

    Techniques: HC2 Assay