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Thermo Fisher hla dqb1
GMTs associated with different <t>HLA-DRB1,</t> -DPB1 , and <t>-DQB1</t> alleles in the IJEV NAb-positive group.
Hla Dqb1, supplied by Thermo Fisher, used in various techniques. Bioz Stars score: 91/100, based on 1348 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Images

1) Product Images from "HLA Class II Genes HLA-DRB1, HLA-DPB1, and HLA-DQB1 Are Associated With the Antibody Response to Inactivated Japanese Encephalitis Vaccine"

Article Title: HLA Class II Genes HLA-DRB1, HLA-DPB1, and HLA-DQB1 Are Associated With the Antibody Response to Inactivated Japanese Encephalitis Vaccine

Journal: Frontiers in Immunology

doi: 10.3389/fimmu.2019.00428

GMTs associated with different HLA-DRB1, -DPB1 , and -DQB1 alleles in the IJEV NAb-positive group.
Figure Legend Snippet: GMTs associated with different HLA-DRB1, -DPB1 , and -DQB1 alleles in the IJEV NAb-positive group.

Techniques Used:

2) Product Images from "Rotavirus VP2 Core Shell Regions Critical for Viral Polymerase Activation ▿Rotavirus VP2 Core Shell Regions Critical for Viral Polymerase Activation ▿ †"

Article Title: Rotavirus VP2 Core Shell Regions Critical for Viral Polymerase Activation ▿Rotavirus VP2 Core Shell Regions Critical for Viral Polymerase Activation ▿ †

Journal: Journal of Virology

doi: 10.1128/JVI.02360-10

Fivefold hub chimeric VP2 proteins. (A) Cartoon schematics of wild-type and chimeric VP2 proteins. Wild-type SA11 and Bristol VP2 proteins are shown in white and gray, respectively. The residues contributing to the 5-fold hub are delineated from those of the principal domain by a black line. Schematics of the 5-fold hub chimeras (Br:SA and SA:Br) are shown, with the parental origin of amino acids indicated by color (white for SA11 or gray for Bristol). The three amino acids before and after the fusion site are listed. (B) Purified VP2 proteins. VP2 proteins were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular size markers are shown (kilodaltons). (C) In vitro dsRNA synthesis by SA11 or Bristol VP1. Reactions proceeded in the absence (none) or the presence of the different core shell proteins listed above the gels. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography.
Figure Legend Snippet: Fivefold hub chimeric VP2 proteins. (A) Cartoon schematics of wild-type and chimeric VP2 proteins. Wild-type SA11 and Bristol VP2 proteins are shown in white and gray, respectively. The residues contributing to the 5-fold hub are delineated from those of the principal domain by a black line. Schematics of the 5-fold hub chimeras (Br:SA and SA:Br) are shown, with the parental origin of amino acids indicated by color (white for SA11 or gray for Bristol). The three amino acids before and after the fusion site are listed. (B) Purified VP2 proteins. VP2 proteins were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular size markers are shown (kilodaltons). (C) In vitro dsRNA synthesis by SA11 or Bristol VP1. Reactions proceeded in the absence (none) or the presence of the different core shell proteins listed above the gels. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography.

Techniques Used: Purification, Staining, In Vitro, Autoradiography

Truncation mutagenesis of the SA11 VP2 5-fold hub. (A) Cartoon schematics of wild-type and mutant SA11 VP2 proteins. The residues contributing to the 5-fold hub are delineated from those of the principal domain by a black line. The three amino acids that follow the starting methionine are listed for the wild type (SA11) and each mutant protein (Δ10, Δ36, and Δ102). (B) Purified VP2 proteins. VP2 proteins were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular size markers are shown (in kilodaltons). (C) In vitro dsRNA synthesis by SA11 VP1. Reactions proceeded in the absence (none) or the presence of the different core shell proteins listed above the gel. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography.
Figure Legend Snippet: Truncation mutagenesis of the SA11 VP2 5-fold hub. (A) Cartoon schematics of wild-type and mutant SA11 VP2 proteins. The residues contributing to the 5-fold hub are delineated from those of the principal domain by a black line. The three amino acids that follow the starting methionine are listed for the wild type (SA11) and each mutant protein (Δ10, Δ36, and Δ102). (B) Purified VP2 proteins. VP2 proteins were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular size markers are shown (in kilodaltons). (C) In vitro dsRNA synthesis by SA11 VP1. Reactions proceeded in the absence (none) or the presence of the different core shell proteins listed above the gel. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography.

Techniques Used: Mutagenesis, Purification, Staining, In Vitro, Autoradiography

Genetic divergence of VP1 and VP2 from different rotavirus strains. Phylogenetic dendrograms of VP1 (top) or VP2 (bottom) were constructed by using the amino acid sequences and the neighbor-joining method (1,000 bootstrap repetitions). The virus strain is listed with the species of isolation in parentheses: human (hu), simian (si), bovine (bo), porcine (po), feline (fe), canine (ca), murine (mu), and avian (av). The proteins of a group B rotavirus (strain WH-1) were used to root the trees. Bootstrap values are shown as percentages for key nodes. Brackets indicate the designated category (category I, II, III, or IV) of the VP1 and VP2 proteins. The average intra- and intercategory percent amino acid identities (identity values) are shown in the inset tables. The scale bar represents the number of substitutions per amino acid position.
Figure Legend Snippet: Genetic divergence of VP1 and VP2 from different rotavirus strains. Phylogenetic dendrograms of VP1 (top) or VP2 (bottom) were constructed by using the amino acid sequences and the neighbor-joining method (1,000 bootstrap repetitions). The virus strain is listed with the species of isolation in parentheses: human (hu), simian (si), bovine (bo), porcine (po), feline (fe), canine (ca), murine (mu), and avian (av). The proteins of a group B rotavirus (strain WH-1) were used to root the trees. Bootstrap values are shown as percentages for key nodes. Brackets indicate the designated category (category I, II, III, or IV) of the VP1 and VP2 proteins. The average intra- and intercategory percent amino acid identities (identity values) are shown in the inset tables. The scale bar represents the number of substitutions per amino acid position.

Techniques Used: Construct, Isolation

Structure of the rotavirus VP2 core shell. (Left) Structure of the T=1 icosahedral core shell of bovine rotavirus (PDB accession number 3KZ4), with each of the 120 VP2 monomers depicted in a surface representation. Five type A and five type B VP2 monomers of a central decamer are in dark blue and light blue, respectively. (Right) Inside view of two neighboring VP2 A-B dimers. Type A and B monomers are in dark blue and light blue, respectively. One of the dimers (comprised of monomers A1 and B1) is depicted in a ribbon representation, while the other (comprised of monomers A2 and B2) is depicted in a surface representation. The resolved portion of the VP2 amino terminus in type B monomers (residues 81 to 100) is yellow and is shown in a ribbon representation.
Figure Legend Snippet: Structure of the rotavirus VP2 core shell. (Left) Structure of the T=1 icosahedral core shell of bovine rotavirus (PDB accession number 3KZ4), with each of the 120 VP2 monomers depicted in a surface representation. Five type A and five type B VP2 monomers of a central decamer are in dark blue and light blue, respectively. (Right) Inside view of two neighboring VP2 A-B dimers. Type A and B monomers are in dark blue and light blue, respectively. One of the dimers (comprised of monomers A1 and B1) is depicted in a ribbon representation, while the other (comprised of monomers A2 and B2) is depicted in a surface representation. The resolved portion of the VP2 amino terminus in type B monomers (residues 81 to 100) is yellow and is shown in a ribbon representation.

Techniques Used:

Functional compatibility of VP1 and VP2 proteins. (A) Purified VP1 and VP2 proteins. Recombinant proteins were expressed in insect cells using baculovirus vectors and purified as described in Materials and Methods. The designated category (category I, II, III, or IV) of each protein is shown in parentheses above the strain. Samples containing approximately 2 pmol of VP1 or 20 pmol of VP2 were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular mass markers are shown (in kilodaltons). (B) In vitro dsRNA synthesis by SA11 (top), PO-13 (middle), or Bristol (bottom) VP1. The designated category (category I, III, or IV) of each polymerase is shown in parentheses above the strain. Reactions proceeded in the absence (none) or presence of the different core shell proteins listed above the gels. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography. The images on the left represent 4-h exposures (exp) of the gels to film. To visualize SA11 VP1 activity in the presence of PO-13 VP2, the gel was exposed to film for 24 h.
Figure Legend Snippet: Functional compatibility of VP1 and VP2 proteins. (A) Purified VP1 and VP2 proteins. Recombinant proteins were expressed in insect cells using baculovirus vectors and purified as described in Materials and Methods. The designated category (category I, II, III, or IV) of each protein is shown in parentheses above the strain. Samples containing approximately 2 pmol of VP1 or 20 pmol of VP2 were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular mass markers are shown (in kilodaltons). (B) In vitro dsRNA synthesis by SA11 (top), PO-13 (middle), or Bristol (bottom) VP1. The designated category (category I, III, or IV) of each polymerase is shown in parentheses above the strain. Reactions proceeded in the absence (none) or presence of the different core shell proteins listed above the gels. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography. The images on the left represent 4-h exposures (exp) of the gels to film. To visualize SA11 VP1 activity in the presence of PO-13 VP2, the gel was exposed to film for 24 h.

Techniques Used: Functional Assay, Purification, Recombinant, Staining, In Vitro, Autoradiography, Activity Assay

Subdomain chimeric VP2 proteins. (A) Ribbon representation of neighboring VP2 monomers in a dimeric unit (inside view). The apical, central, and dimer-forming subdomains are in blue, green, and red, respectively. The resolved portion of the VP2 amino terminus in the type B monomer (residues 81 to 100) is in yellow. (B) Surface representations of chimeric (CHIM) VP2 proteins. In all images, gray indicates Bristol VP2 residues, while color indicates SA11 VP2 residues. (C) Purified VP2 proteins. VP2 proteins were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular size markers are shown (in kilodaltons). (D) In vitro dsRNA synthesis by SA11 or Bristol VP1. Reactions proceeded in the absence (none) or the presence of the different core shell proteins listed above the gel. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography.
Figure Legend Snippet: Subdomain chimeric VP2 proteins. (A) Ribbon representation of neighboring VP2 monomers in a dimeric unit (inside view). The apical, central, and dimer-forming subdomains are in blue, green, and red, respectively. The resolved portion of the VP2 amino terminus in the type B monomer (residues 81 to 100) is in yellow. (B) Surface representations of chimeric (CHIM) VP2 proteins. In all images, gray indicates Bristol VP2 residues, while color indicates SA11 VP2 residues. (C) Purified VP2 proteins. VP2 proteins were electrophoresed in a 10% SDS-polyacrylamide gel and visualized by PageBlue staining. Molecular size markers are shown (in kilodaltons). (D) In vitro dsRNA synthesis by SA11 or Bristol VP1. Reactions proceeded in the absence (none) or the presence of the different core shell proteins listed above the gel. Radiolabeled dsRNA products were resolved with 10% SDS-polyacrylamide gels and detected by autoradiography.

Techniques Used: Purification, Staining, In Vitro, Autoradiography

3) Product Images from "Hepatitis E Virus (HEV) Strains in Serum Samples Can Replicate Efficiently in Cultured Cells Despite the Coexistence of HEV Antibodies: Characterization of HEV Virions in Blood Circulation ▿"

Article Title: Hepatitis E Virus (HEV) Strains in Serum Samples Can Replicate Efficiently in Cultured Cells Despite the Coexistence of HEV Antibodies: Characterization of HEV Virions in Blood Circulation ▿

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.02002-09

(a) Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a serum sample (S1) with a viral load of 5.0 × 10 5 copies/ml that had been mixed with a pooled serum sample obtained during the early convalescent phase (pool 1, 2, or 3) and positive for IgM-, IgA-, and IgG-class anti-HEV antibodies or with an antibody-negative serum and cultured for 50 days. (b) Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a serum sample (S1) with a viral load of 5.0 × 10 5 ) at a final concentration of 1 mg/ml and cultured for 50 days. (c) Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a fecal suspension (JE03-1760F), a serum sample (S4a), or a culture supernatant of JE03-1760F (patient 4) origin with an HEV load of 2.0 × 10 5 copies/ml that had been mixed with a serum sample (03-2150) positive for IgM-, IgA-, and IgG-class anti-HEV antibodies but negative for HEV RNA, another serum sample (08-1340) positive only for IgG anti-HEV, or an antibody-negative serum and cultured for the indicated number of days. The fecal suspension, serum sample (S4a), and culture supernatant contained HEV of the same strain (JE03-1760F), and serum samples (S4a, 03-2150, and 08-1340) were obtained from the JE03-1760F patient (patient 4 in this study) 15, 40, and 2,088 days, respectively, after disease onset.
Figure Legend Snippet: (a) Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a serum sample (S1) with a viral load of 5.0 × 10 5 copies/ml that had been mixed with a pooled serum sample obtained during the early convalescent phase (pool 1, 2, or 3) and positive for IgM-, IgA-, and IgG-class anti-HEV antibodies or with an antibody-negative serum and cultured for 50 days. (b) Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a serum sample (S1) with a viral load of 5.0 × 10 5 ) at a final concentration of 1 mg/ml and cultured for 50 days. (c) Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a fecal suspension (JE03-1760F), a serum sample (S4a), or a culture supernatant of JE03-1760F (patient 4) origin with an HEV load of 2.0 × 10 5 copies/ml that had been mixed with a serum sample (03-2150) positive for IgM-, IgA-, and IgG-class anti-HEV antibodies but negative for HEV RNA, another serum sample (08-1340) positive only for IgG anti-HEV, or an antibody-negative serum and cultured for the indicated number of days. The fecal suspension, serum sample (S4a), and culture supernatant contained HEV of the same strain (JE03-1760F), and serum samples (S4a, 03-2150, and 08-1340) were obtained from the JE03-1760F patient (patient 4 in this study) 15, 40, and 2,088 days, respectively, after disease onset.

Techniques Used: Quantitation Assay, Cell Culture, Concentration Assay

Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a culture supernatant with a viral load of 1.0 × 10 5 copies/ml that had been treated with or without 0.1% NP-40 and 0.1% pronase E, mixed with a normal serum or pooled serum sample obtained at the early convalescent phase (pool 1) and positive for IgM-, IgA-, and IgG-class anti-HEV ORF2 and ORF3 antibodies, and cultured for 30 days.
Figure Legend Snippet: Quantitation of HEV RNA in culture supernatants of A549 cells inoculated with a culture supernatant with a viral load of 1.0 × 10 5 copies/ml that had been treated with or without 0.1% NP-40 and 0.1% pronase E, mixed with a normal serum or pooled serum sample obtained at the early convalescent phase (pool 1) and positive for IgM-, IgA-, and IgG-class anti-HEV ORF2 and ORF3 antibodies, and cultured for 30 days.

Techniques Used: Quantitation Assay, Cell Culture

4) Product Images from "MDR1 polymorphisms effect cyclosporine AUC0-4 values in Beh?et's disease patients"

Article Title: MDR1 polymorphisms effect cyclosporine AUC0-4 values in Beh?et's disease patients

Journal: Clinical ophthalmology (Auckland, N.Z.)

doi:

Correlation of the MDR1 exon 21 SNP with dose normalized cyclosporine AUC(0-4). AUC(0-4) values were 485 ± 206 ng · hr/ml in G/G genotype, 523 ± 189 ng · hr/ml in G/T genotype, 856 ± 122 ng · hr/ml in T/T, A/A genotype, T/T and A/A which are mutant homozygotes had higher AUC0-4 than G/G genotype. (p = 0.008, 0.019).
Figure Legend Snippet: Correlation of the MDR1 exon 21 SNP with dose normalized cyclosporine AUC(0-4). AUC(0-4) values were 485 ± 206 ng · hr/ml in G/G genotype, 523 ± 189 ng · hr/ml in G/T genotype, 856 ± 122 ng · hr/ml in T/T, A/A genotype, T/T and A/A which are mutant homozygotes had higher AUC0-4 than G/G genotype. (p = 0.008, 0.019).

Techniques Used: Mutagenesis

Correlation of the MDR1 promoter region polymorphisms with dose normalized cyclosporine AUC0-4. Promoter types 1/1, 1/4, and 1/6 had high AUC0-4 levels, types 1/2, 1/5, 2/4 had low AUC0-4 levels, and heterozygote of haplotype 1/2, compared to 1/1 and 1/4 had significantly lower AUC0-4 levels. (p = 0.007 and 0.049).
Figure Legend Snippet: Correlation of the MDR1 promoter region polymorphisms with dose normalized cyclosporine AUC0-4. Promoter types 1/1, 1/4, and 1/6 had high AUC0-4 levels, types 1/2, 1/5, 2/4 had low AUC0-4 levels, and heterozygote of haplotype 1/2, compared to 1/1 and 1/4 had significantly lower AUC0-4 levels. (p = 0.007 and 0.049).

Techniques Used:

Correlation of the MDR1 exon 26 SNP with dose normalized cyclosporine AUC0-4. AUC0-4 values were 449 ± 195 ng · hr/ml in those with C/C in the C3435T, 666 ± 256 ng · hr/ml in those with C/T, 704 ± 142 ng · hr/ml in those with T/T genotype. C homozygotes tended to have lower AUC0-4 than other types. (p = 0.101, p = 0.079).
Figure Legend Snippet: Correlation of the MDR1 exon 26 SNP with dose normalized cyclosporine AUC0-4. AUC0-4 values were 449 ± 195 ng · hr/ml in those with C/C in the C3435T, 666 ± 256 ng · hr/ml in those with C/T, 704 ± 142 ng · hr/ml in those with T/T genotype. C homozygotes tended to have lower AUC0-4 than other types. (p = 0.101, p = 0.079).

Techniques Used:

5) Product Images from "Effects of Cellular Pathway Disturbances on Misfolded Superoxide Dismutase-1 in Fibroblasts Derived from ALS Patients"

Article Title: Effects of Cellular Pathway Disturbances on Misfolded Superoxide Dismutase-1 in Fibroblasts Derived from ALS Patients

Journal: PLoS ONE

doi: 10.1371/journal.pone.0150133

Inhibition of proteasome causes accumulation of detergent-insoluble SOD1 aggregates. Fibroblast cell lines were cultured in the absence (-) and presence (+) of bortezomib (5 ng/ml) for 24 h. Detergent insoluble fractions were analysed by western blotting using the anti-SOD1 (57–72 aa) antibody. No insoluble aggregates were seen in the control and D90A lines. Proteasome inhibition increased the amount of aggregates in G93A, A4V, H46R, G127X and D125Tfs*24 lines.
Figure Legend Snippet: Inhibition of proteasome causes accumulation of detergent-insoluble SOD1 aggregates. Fibroblast cell lines were cultured in the absence (-) and presence (+) of bortezomib (5 ng/ml) for 24 h. Detergent insoluble fractions were analysed by western blotting using the anti-SOD1 (57–72 aa) antibody. No insoluble aggregates were seen in the control and D90A lines. Proteasome inhibition increased the amount of aggregates in G93A, A4V, H46R, G127X and D125Tfs*24 lines.

Techniques Used: Inhibition, Cell Culture, Western Blot

Effect of induction of ER stress and perturbation of mitochondria on the levels of misfolded and total SOD1 in fibroblast lines. Misfolded and total SOD1 in lysates of fibroblasts were analysed with the 24–39 misELISA and ELISA for total SOD1, respectively. Fibroblast cell lines were cultured in triplicate for 24 h in the absence (blue) and presence (red) of the ER-stress inducer tunicamycin (A-C; 0.5 μg/ml) and the mitochondrial inhibitor rotenone (D-F; 5 μM). Data is expressed as the mean ± SD (n = 3), * p
Figure Legend Snippet: Effect of induction of ER stress and perturbation of mitochondria on the levels of misfolded and total SOD1 in fibroblast lines. Misfolded and total SOD1 in lysates of fibroblasts were analysed with the 24–39 misELISA and ELISA for total SOD1, respectively. Fibroblast cell lines were cultured in triplicate for 24 h in the absence (blue) and presence (red) of the ER-stress inducer tunicamycin (A-C; 0.5 μg/ml) and the mitochondrial inhibitor rotenone (D-F; 5 μM). Data is expressed as the mean ± SD (n = 3), * p

Techniques Used: Enzyme-linked Immunosorbent Assay, Cell Culture

Effect of reduction in the activities of the proteasome and autophagy on the levels of misfolded and total SOD1 in fibroblast lines. Misfolded and total SOD1 in lysates of fibroblasts were analysed with the 24–39 misELISA and ELISA for total SOD1, respectively. Fibroblast cell lines were cultured in triplicate for 24 h in the absence (blue) or the presence (red) of the proteasome inhibitor bortezomib (A-C; 5 ng/ml), the autophagy inhibitor 3-MA (D-F; 10 mM). Data is expressed as the mean ± SD (n = 3), * p
Figure Legend Snippet: Effect of reduction in the activities of the proteasome and autophagy on the levels of misfolded and total SOD1 in fibroblast lines. Misfolded and total SOD1 in lysates of fibroblasts were analysed with the 24–39 misELISA and ELISA for total SOD1, respectively. Fibroblast cell lines were cultured in triplicate for 24 h in the absence (blue) or the presence (red) of the proteasome inhibitor bortezomib (A-C; 5 ng/ml), the autophagy inhibitor 3-MA (D-F; 10 mM). Data is expressed as the mean ± SD (n = 3), * p

Techniques Used: Enzyme-linked Immunosorbent Assay, Cell Culture

SOD1 protein in lysates of fibroblast cultures. (A) Fibroblast lysates were analysed by western blotting using the anti-SOD1 (57–72 aa) antibody. β-actin was used as a loading control. The band of the truncated G127X mutant was not visible except in the presence of the proteasome inhibitor bortezomib (arrow). The homozygous D90A mutant displays increased mobility. (B) The expression of SOD1 in the fibroblast lines were compared as SOD1/β-actin ratios. The mean of the 2 control lines was taken as 1. Three replicate sets of fibroblast cultures were analyzed. The data are expressed as means ± SD. (*) p
Figure Legend Snippet: SOD1 protein in lysates of fibroblast cultures. (A) Fibroblast lysates were analysed by western blotting using the anti-SOD1 (57–72 aa) antibody. β-actin was used as a loading control. The band of the truncated G127X mutant was not visible except in the presence of the proteasome inhibitor bortezomib (arrow). The homozygous D90A mutant displays increased mobility. (B) The expression of SOD1 in the fibroblast lines were compared as SOD1/β-actin ratios. The mean of the 2 control lines was taken as 1. Three replicate sets of fibroblast cultures were analyzed. The data are expressed as means ± SD. (*) p

Techniques Used: Western Blot, Mutagenesis, Expressing

6) Product Images from "Bacterial treatment of alkaline cement kiln dust using Bacillus halodurans strain KG1"

Article Title: Bacterial treatment of alkaline cement kiln dust using Bacillus halodurans strain KG1

Journal: Brazilian Journal of Microbiology

doi: 10.1016/j.bjm.2015.11.001

A neighbor-joining phylogenetic tree showing the relationships of bacterial strain KG1 and the type strains of closely related Bacillus species, based on 16S rRNA gene sequences. The GenBank accession numbers are given in parentheses. Bootstrap values (expressed as percentages of 1000 replications) greater than 50% are shown at the branch points. Bar, 0.02 nucleotide substitutions per site.
Figure Legend Snippet: A neighbor-joining phylogenetic tree showing the relationships of bacterial strain KG1 and the type strains of closely related Bacillus species, based on 16S rRNA gene sequences. The GenBank accession numbers are given in parentheses. Bootstrap values (expressed as percentages of 1000 replications) greater than 50% are shown at the branch points. Bar, 0.02 nucleotide substitutions per site.

Techniques Used:

7) Product Images from "Extracellular and Mixotrophic Symbiosis in the Whale-Fall Mussel Adipicola pacifica: A Trend in Evolution from Extra- to Intracellular Symbiosis"

Article Title: Extracellular and Mixotrophic Symbiosis in the Whale-Fall Mussel Adipicola pacifica: A Trend in Evolution from Extra- to Intracellular Symbiosis

Journal: PLoS ONE

doi: 10.1371/journal.pone.0011808

Phylogeny of bacterial symbionts from whale-fall Adipicola mussels based on 16S rRNA gene sequences. Bayesian (BA) tree of the γ-Proteobacteria are shown. Scale bar represents 0.05 nucleotide substitution per sequence position. A BA posterior probability greater than 0.5 and bootstrap values greater than 50% are shown for each branch, with left, center and middle values representing posterior probability in BA and bootstrap values in the maximum-likelihood (ML) and neighbor-joining (NJ) methods, respectively. Symbionts of the mussels examined in this study are highlighted. The accession numbers used for this study are shown in parentheses following the operational taxonomic unit names.
Figure Legend Snippet: Phylogeny of bacterial symbionts from whale-fall Adipicola mussels based on 16S rRNA gene sequences. Bayesian (BA) tree of the γ-Proteobacteria are shown. Scale bar represents 0.05 nucleotide substitution per sequence position. A BA posterior probability greater than 0.5 and bootstrap values greater than 50% are shown for each branch, with left, center and middle values representing posterior probability in BA and bootstrap values in the maximum-likelihood (ML) and neighbor-joining (NJ) methods, respectively. Symbionts of the mussels examined in this study are highlighted. The accession numbers used for this study are shown in parentheses following the operational taxonomic unit names.

Techniques Used: Sequencing

8) Product Images from "Association between colony-stimulating factor 1 receptor gene polymorphisms and asthma risk"

Article Title: Association between colony-stimulating factor 1 receptor gene polymorphisms and asthma risk

Journal: Human Genetics

doi: 10.1007/s00439-010-0850-3

Gene map, p value, haplotype list, and linkage disequilibrium of SNPs in the CSF1R gene. a Log p values for the association analysis of SNPs with asthma risk. b Gene map and locations of the SNPs in the CSF1R gene at chromosome 5q33–q35 (60 kb). The first base of the translation start site is denoted as nucleotide +1. The black and white blocks represent the untranslated regions and coding regions of CSF1R , respectively. *polymorphisms selected for large-scale genotyping, considering allele frequencies, locations, and LD after discovery. **SNPs selected in the HapMap database. p values of each SNP were demonstrated in three different models (co-dominant, dominant, and recessive). c Haplotypes of CSF1R . d Linkage disequilibrium coefficient (| D ′| and r 2 ) among CSF1R SNPs
Figure Legend Snippet: Gene map, p value, haplotype list, and linkage disequilibrium of SNPs in the CSF1R gene. a Log p values for the association analysis of SNPs with asthma risk. b Gene map and locations of the SNPs in the CSF1R gene at chromosome 5q33–q35 (60 kb). The first base of the translation start site is denoted as nucleotide +1. The black and white blocks represent the untranslated regions and coding regions of CSF1R , respectively. *polymorphisms selected for large-scale genotyping, considering allele frequencies, locations, and LD after discovery. **SNPs selected in the HapMap database. p values of each SNP were demonstrated in three different models (co-dominant, dominant, and recessive). c Haplotypes of CSF1R . d Linkage disequilibrium coefficient (| D ′| and r 2 ) among CSF1R SNPs

Techniques Used:

9) Product Images from "A FRMD7 variant in a Japanese family causes congenital nystagmus"

Article Title: A FRMD7 variant in a Japanese family causes congenital nystagmus

Journal: Human Genome Variation

doi: 10.1038/hgv.2015.2

A Japanese family with X-linked congenital nystagmus. ( a ) Pedigree. The squares and circle represent males and female, respectively. Black symbols indicate affected individuals, and unfilled symbols indicate unaffected individuals. Arrow marks the proband. ( b ) DNA sequence chromatograms of the FRMD7 . Affected family members are denoted by II:1, II:2 and II:3. Arrow marks the variant, c.875T > C. ( c ) Cross-species multiple alignment of FRMD7 protein sequences around the pL292P variant site, showing evolutionary conservation of the altered residue in the highly conserved residues of the FERM-adjacent (FA) domain . Amino-acid sequence comparison in several related proteins using ClustalW2 ( http://www.ebi.ac.uk/Tools/msa/clustalw2/ ). The nine proteins depicted are from human, Pan troglodytes , Macaca mulatta , Mus musculus , Rattus norvegicus , Canis familiaris , Bos taurus , Equus caballus and Gallus gallus. The FRMD7 variant, p.L292P, is indicated above the aligned sequence, with the amino acid shaded in the alignment. Arrow heads indicate residues reported to be causative mutations around codon 292 in cases with XLICN. 14–20 Gray bars indicate regions of the FERM and FA domains.
Figure Legend Snippet: A Japanese family with X-linked congenital nystagmus. ( a ) Pedigree. The squares and circle represent males and female, respectively. Black symbols indicate affected individuals, and unfilled symbols indicate unaffected individuals. Arrow marks the proband. ( b ) DNA sequence chromatograms of the FRMD7 . Affected family members are denoted by II:1, II:2 and II:3. Arrow marks the variant, c.875T > C. ( c ) Cross-species multiple alignment of FRMD7 protein sequences around the pL292P variant site, showing evolutionary conservation of the altered residue in the highly conserved residues of the FERM-adjacent (FA) domain . Amino-acid sequence comparison in several related proteins using ClustalW2 ( http://www.ebi.ac.uk/Tools/msa/clustalw2/ ). The nine proteins depicted are from human, Pan troglodytes , Macaca mulatta , Mus musculus , Rattus norvegicus , Canis familiaris , Bos taurus , Equus caballus and Gallus gallus. The FRMD7 variant, p.L292P, is indicated above the aligned sequence, with the amino acid shaded in the alignment. Arrow heads indicate residues reported to be causative mutations around codon 292 in cases with XLICN. 14–20 Gray bars indicate regions of the FERM and FA domains.

Techniques Used: Sequencing, Variant Assay

10) Product Images from "Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans"

Article Title: Presence of Extensive Wolbachia Symbiont Insertions Discovered in the Genome of Its Host Glossina morsitans morsitans

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0002728

16S rRNA , fbpA and wsp gene fragments from tsetse Wolbachia chromosomal insertions sequenced from Gmm laboratory and natural populations aligned with the corresponding regions of w Gmm. Black lines represent the deleted region. The numbers show the positions before and after the deletions in respect to the w Mel genome and the right-left white arrows below the number indicate the size of deletion in base pairs.
Figure Legend Snippet: 16S rRNA , fbpA and wsp gene fragments from tsetse Wolbachia chromosomal insertions sequenced from Gmm laboratory and natural populations aligned with the corresponding regions of w Gmm. Black lines represent the deleted region. The numbers show the positions before and after the deletions in respect to the w Mel genome and the right-left white arrows below the number indicate the size of deletion in base pairs.

Techniques Used:

Fluorescent in situ hybridisation (FISH) on Gmm mitotic chromosomes. The chromosomes are numbered as described by Willhoeft (1997) [70] . A–B. Banding pattern of (DAPI)-stained chromosome spreads (A–B). The DAPI positive regions indicate the heterochromatic patterns. B-chromosomes vary in number. FISH on female and male chromosomes with fbpA probe (C–D), 16S rDNA probe (E–F), and wsp probe on chromosomes from a male individual (G).
Figure Legend Snippet: Fluorescent in situ hybridisation (FISH) on Gmm mitotic chromosomes. The chromosomes are numbered as described by Willhoeft (1997) [70] . A–B. Banding pattern of (DAPI)-stained chromosome spreads (A–B). The DAPI positive regions indicate the heterochromatic patterns. B-chromosomes vary in number. FISH on female and male chromosomes with fbpA probe (C–D), 16S rDNA probe (E–F), and wsp probe on chromosomes from a male individual (G).

Techniques Used: In Situ, Hybridization, Fluorescence In Situ Hybridization, Staining

11) Product Images from "Studies on Aphis gossypii cytochrome P450s CYP6CY22 and CYP6CY13 using an in vitro system"

Article Title: Studies on Aphis gossypii cytochrome P450s CYP6CY22 and CYP6CY13 using an in vitro system

Journal: Journal of Pesticide Science

doi: 10.1584/jpestics.D17-006

Fig. 2. Expression of A. gossypii CYP6CY22 and CYP6CY13 genes in transfected D. melanogaster S2 cells. Lane 1=molecular weight standards. Lanes 2 and 5=negative control, cells transfect ed only with the pAc5.1 vector without inserted genes. Lanes 3 and 4=cells transfected with c21228_g1 and c21368_g1 genes and cultured in normal medium (Schneider’s Drosophila Medium with 10% FBS). Lanes 6 and 7=cells transfected with c21228_g1 and c21368_g1 genes (59 kDa) and cultured in CYP expression medium (Insectagro DS2 medium supplemented with 0.1 mM ferric citrate, 0.1 mM 5-aminolevulinic acid, and 4 mM Ala-Glu without FBS).
Figure Legend Snippet: Fig. 2. Expression of A. gossypii CYP6CY22 and CYP6CY13 genes in transfected D. melanogaster S2 cells. Lane 1=molecular weight standards. Lanes 2 and 5=negative control, cells transfect ed only with the pAc5.1 vector without inserted genes. Lanes 3 and 4=cells transfected with c21228_g1 and c21368_g1 genes and cultured in normal medium (Schneider’s Drosophila Medium with 10% FBS). Lanes 6 and 7=cells transfected with c21228_g1 and c21368_g1 genes (59 kDa) and cultured in CYP expression medium (Insectagro DS2 medium supplemented with 0.1 mM ferric citrate, 0.1 mM 5-aminolevulinic acid, and 4 mM Ala-Glu without FBS).

Techniques Used: Expressing, Transfection, Molecular Weight, Negative Control, Plasmid Preparation, Cell Culture

12) Product Images from "Genes WHEAT FRIZZY PANICLE and SHAM RAMIFICATION 2 independently regulate differentiation of floral meristems in wheat"

Article Title: Genes WHEAT FRIZZY PANICLE and SHAM RAMIFICATION 2 independently regulate differentiation of floral meristems in wheat

Journal: BMC Plant Biology

doi: 10.1186/s12870-017-1191-3

Ramified spike and turgidum -type of spike branching in tetraploid wheats. a , Illustration of structure of standard spike (WT) in T. durum LD222 (left), ramified spike (indicated as gradation from horizontal spikelets, HS, to ramified spike, RS) in T. durum R-107 (middle) and the turgidum -type of spike branching (indicated as branched head, BH t ) in T. turgidum K-40750 (right). b , Schematic representation of the WFZP-A gene structures and the mutation identified. The light red box indicates the AP2/ERF domain. c - k , Scanning electron microscopy images of LD222 (WT), R-107 ( bh ) and K-40750 ( bh t ) inflorescences at various developmental stages. c and d , Spikelet differentiation stage in the wild type ( c ) and bh ( d ). e , Early floret differentiation stages when the spikelet meristem produces FMs in WT. f , Differentiation of secondary AxMs (indicated by asterisks) in the bh mutant. h and i , The development of glumes (gl*, indicated by arrows) and floret meristems (fm*s) by secondary AxMs in the bh and bh t mutants. g , Floret differentiation stage in the WT-inflorescence. h , development of an ectopic spikelet at place of a basal floret. j and k , Development of ectopic branch-like structures ( b ) in the bh and bh t mutants. Bars = 100 μm. f , floret with floret organ primordia; fm, floret meristem; gl, glume; im, inflorescence meristem; l, lemma, sm, spikelet meristem; sm*, spikelet meristem of an ectopic spikelet
Figure Legend Snippet: Ramified spike and turgidum -type of spike branching in tetraploid wheats. a , Illustration of structure of standard spike (WT) in T. durum LD222 (left), ramified spike (indicated as gradation from horizontal spikelets, HS, to ramified spike, RS) in T. durum R-107 (middle) and the turgidum -type of spike branching (indicated as branched head, BH t ) in T. turgidum K-40750 (right). b , Schematic representation of the WFZP-A gene structures and the mutation identified. The light red box indicates the AP2/ERF domain. c - k , Scanning electron microscopy images of LD222 (WT), R-107 ( bh ) and K-40750 ( bh t ) inflorescences at various developmental stages. c and d , Spikelet differentiation stage in the wild type ( c ) and bh ( d ). e , Early floret differentiation stages when the spikelet meristem produces FMs in WT. f , Differentiation of secondary AxMs (indicated by asterisks) in the bh mutant. h and i , The development of glumes (gl*, indicated by arrows) and floret meristems (fm*s) by secondary AxMs in the bh and bh t mutants. g , Floret differentiation stage in the WT-inflorescence. h , development of an ectopic spikelet at place of a basal floret. j and k , Development of ectopic branch-like structures ( b ) in the bh and bh t mutants. Bars = 100 μm. f , floret with floret organ primordia; fm, floret meristem; gl, glume; im, inflorescence meristem; l, lemma, sm, spikelet meristem; sm*, spikelet meristem of an ectopic spikelet

Techniques Used: Mutagenesis, Electron Microscopy

13) Product Images from "HSF1 and HSF3 cooperatively regulate the heat shock response in lizards"

Article Title: HSF1 and HSF3 cooperatively regulate the heat shock response in lizards

Journal: PLoS ONE

doi: 10.1371/journal.pone.0180776

Heat shock induces the HSE-binding activity of HSF1 and HSF3 in lizard and frog tissues. ( A ) Expression of HSF1 and HSF3 in lizard tissues. Whole cell extracts were prepared from the brain and heart of control lizard Anolis sagrei maintained at 28 ° C (C), lizards heat-shocked at 42 ° C for 1 h (HS), or the lizards that were heat-shocked and then recovered at 28 ° C for 3 h. Aliquots (80 μg proteins) were subjected to western blotting using anti-HSF1 (anti-cHSF1x), anti-HSF3 (anti-AsHSF3-1), or anti-β-actin antibodies. ( B ) Induction of the HSE-binding activity in lizard tissues during heat shock. Aliquots (20 μg proteins) of whole cell extracts described in A were subjected to EMSA. An arrowhead indicates the HSF:HSE complex. ( C ) Analysis of heat-induced HSE-binding activity. Whole cell extracts from the tissues described in A (20 μg proteins) were subjected to antibody supershift experiments using anti-HSF1 (anti-cHSF1γ), anti-HSF2 (anti-mHSF2-4), or anti-HSF3 (anti-AsHSF3-1) antibodies, or preimmune (PI) serum. Each 1:10-diluted antiserum (2 μl) was added in the binding mixture. ( D ) Expression of HSF1 and HSF3 in frog tissues. Whole cell extracts were prepared from the brain and heart of control frog Xenopus tropicalis maintained at 25 ° C (C), the lizard heat-shocked at 31 ° C for 1 h (HS1) or at 33 ° C for 1 h (HS2). Aliquots (80 μg proteins) were subjected to western blotting using anti-HSF1 (anti-cHSF1x), anti-HSF3 (anti-XtHSF3-2), or anti-β-actin antibodies. ( E ) Induction of HSE-binding activity in frog tissues during heat shock. Aliquots (20 μg proteins) of whole cell extracts described in D were subjected to EMSA. ( F ) Analysis of heat-induced HSE-binding activity. Whole cell extracts from the tissues described in D (20 μg proteins) were subjected to antibody supershift experiments using anti-HSF1 (anti-cHSF1γ), anti-HSF2 (anti-mHSF2-4), or anti-HSF3 (anti-XtHSF3-2) antibodies, or preimmune (PI) serum.
Figure Legend Snippet: Heat shock induces the HSE-binding activity of HSF1 and HSF3 in lizard and frog tissues. ( A ) Expression of HSF1 and HSF3 in lizard tissues. Whole cell extracts were prepared from the brain and heart of control lizard Anolis sagrei maintained at 28 ° C (C), lizards heat-shocked at 42 ° C for 1 h (HS), or the lizards that were heat-shocked and then recovered at 28 ° C for 3 h. Aliquots (80 μg proteins) were subjected to western blotting using anti-HSF1 (anti-cHSF1x), anti-HSF3 (anti-AsHSF3-1), or anti-β-actin antibodies. ( B ) Induction of the HSE-binding activity in lizard tissues during heat shock. Aliquots (20 μg proteins) of whole cell extracts described in A were subjected to EMSA. An arrowhead indicates the HSF:HSE complex. ( C ) Analysis of heat-induced HSE-binding activity. Whole cell extracts from the tissues described in A (20 μg proteins) were subjected to antibody supershift experiments using anti-HSF1 (anti-cHSF1γ), anti-HSF2 (anti-mHSF2-4), or anti-HSF3 (anti-AsHSF3-1) antibodies, or preimmune (PI) serum. Each 1:10-diluted antiserum (2 μl) was added in the binding mixture. ( D ) Expression of HSF1 and HSF3 in frog tissues. Whole cell extracts were prepared from the brain and heart of control frog Xenopus tropicalis maintained at 25 ° C (C), the lizard heat-shocked at 31 ° C for 1 h (HS1) or at 33 ° C for 1 h (HS2). Aliquots (80 μg proteins) were subjected to western blotting using anti-HSF1 (anti-cHSF1x), anti-HSF3 (anti-XtHSF3-2), or anti-β-actin antibodies. ( E ) Induction of HSE-binding activity in frog tissues during heat shock. Aliquots (20 μg proteins) of whole cell extracts described in D were subjected to EMSA. ( F ) Analysis of heat-induced HSE-binding activity. Whole cell extracts from the tissues described in D (20 μg proteins) were subjected to antibody supershift experiments using anti-HSF1 (anti-cHSF1γ), anti-HSF2 (anti-mHSF2-4), or anti-HSF3 (anti-XtHSF3-2) antibodies, or preimmune (PI) serum.

Techniques Used: Binding Assay, Activity Assay, Expressing, Western Blot

14) Product Images from "SNAIL is a key regulator of alveolar rhabdomyosarcoma tumor growth and differentiation through repression of MYF5 and MYOD function"

Article Title: SNAIL is a key regulator of alveolar rhabdomyosarcoma tumor growth and differentiation through repression of MYF5 and MYOD function

Journal: Cell Death & Disease

doi: 10.1038/s41419-018-0693-8

SNAIL is a direct transcriptional repressor of MYF5 expression and regulator of MYOD activity. a SNAIL silencing in RH30 cells induces MYOD binding to GC rich E-Box sequences. Nuclear protein extracts from both undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium supplemented with 2% HS were used in TransAM MyoD DNA-binding ELISA. To monitor the specificity of the assay, the wild-type consensus oligonucleotide (wt) and mutated (mut) sequences were used as competitors for MYOD binding from cell extracts; n = 3. b SNAIL binds to the MYF5 and E-cadherin promoters in RH30 cells. The promoter of MYF5 (~1000 bb) was screened for putative SNAIL transcription factor binding sites and the results were validated by Chip Assay. The images depict one representative result of the ChIP assay. Proteins bound to DNA were immunoprecipitated with the anti-SNAIL antibody, negative IgG control, positive histone H3 control and input DNA control was analyzed. Fragments of the MYF5 and E-cadherin promoters were amplified by PCR and visualized on agarose gels stained with ethidium bromide. c SNAIL silencing by siRNA in RH30 WT cells induces MYF5 promoter activation and luciferase expression when cells are transfected with MYF5@pNL plasmid (luciferase under control with MYF5 promoter), whereas MYOD silencing by siRNA does not exert any effect. SNAIL and MYOD compete for binding to MYF5 promoter in RH30 shSNAIL cells ( d ), RH41 WT ( e ), and RH41 shSNAIL cells ( f ), when cells are transfected with MYF5@pNL plasmid and siRNA against SNAIL, MYOD or siSCR (scrambled siRNA). The data were normalized to mCherry fluorescence level in each well. pNL (luciferase plasmid without promoter) served as a negative control and Ubc@pNL plasmid (luciferase under control of ubiquitin C promoter) was a positive control. The data represent the mean ± SEM or are representative images of at least 3 independent experiments. * p
Figure Legend Snippet: SNAIL is a direct transcriptional repressor of MYF5 expression and regulator of MYOD activity. a SNAIL silencing in RH30 cells induces MYOD binding to GC rich E-Box sequences. Nuclear protein extracts from both undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium supplemented with 2% HS were used in TransAM MyoD DNA-binding ELISA. To monitor the specificity of the assay, the wild-type consensus oligonucleotide (wt) and mutated (mut) sequences were used as competitors for MYOD binding from cell extracts; n = 3. b SNAIL binds to the MYF5 and E-cadherin promoters in RH30 cells. The promoter of MYF5 (~1000 bb) was screened for putative SNAIL transcription factor binding sites and the results were validated by Chip Assay. The images depict one representative result of the ChIP assay. Proteins bound to DNA were immunoprecipitated with the anti-SNAIL antibody, negative IgG control, positive histone H3 control and input DNA control was analyzed. Fragments of the MYF5 and E-cadherin promoters were amplified by PCR and visualized on agarose gels stained with ethidium bromide. c SNAIL silencing by siRNA in RH30 WT cells induces MYF5 promoter activation and luciferase expression when cells are transfected with MYF5@pNL plasmid (luciferase under control with MYF5 promoter), whereas MYOD silencing by siRNA does not exert any effect. SNAIL and MYOD compete for binding to MYF5 promoter in RH30 shSNAIL cells ( d ), RH41 WT ( e ), and RH41 shSNAIL cells ( f ), when cells are transfected with MYF5@pNL plasmid and siRNA against SNAIL, MYOD or siSCR (scrambled siRNA). The data were normalized to mCherry fluorescence level in each well. pNL (luciferase plasmid without promoter) served as a negative control and Ubc@pNL plasmid (luciferase under control of ubiquitin C promoter) was a positive control. The data represent the mean ± SEM or are representative images of at least 3 independent experiments. * p

Techniques Used: Expressing, Activity Assay, Binding Assay, Enzyme-linked Immunosorbent Assay, Chromatin Immunoprecipitation, Immunoprecipitation, Amplification, Polymerase Chain Reaction, Staining, Activation Assay, Luciferase, Transfection, Plasmid Preparation, Fluorescence, Negative Control, Positive Control

15) Product Images from "Evaluation of circulating placenta-related long noncoding RNAs as potential biomarkers for preeclampsia"

Article Title: Evaluation of circulating placenta-related long noncoding RNAs as potential biomarkers for preeclampsia

Journal: Experimental and Therapeutic Medicine

doi: 10.3892/etm.2018.5968

Correlation of placenta-related lncRNAs expression between placenta and plasma. Spearman's rank correlation scatter plot of (A) NONHSAT116812 and (B) NONHSAT145880 levels in placental samples and plasma, which were obtained from 117 pregnant women delivered by C/S (n=42 from early-onset PE group, n=40 from late-onset PE group, and n=35 from control group 1). Data were presented as ΔCq values normalized to GAPDH . lncRNAs, long noncoding RNAs; PE, preeclampsia.
Figure Legend Snippet: Correlation of placenta-related lncRNAs expression between placenta and plasma. Spearman's rank correlation scatter plot of (A) NONHSAT116812 and (B) NONHSAT145880 levels in placental samples and plasma, which were obtained from 117 pregnant women delivered by C/S (n=42 from early-onset PE group, n=40 from late-onset PE group, and n=35 from control group 1). Data were presented as ΔCq values normalized to GAPDH . lncRNAs, long noncoding RNAs; PE, preeclampsia.

Techniques Used: Expressing

Differential expression patterns of placenta-related lncRNAs in PE plasma. Relative expression levels of NONHSAT116812 and NONHSAT145880 in late-onset PE group and control group 1 (n=52 per group) (A) and in early-onset PE group and control group 2 (n=58 per group) (B). 2 −ΔΔCq method was used to calculate lncRNA expression and the expression levels of each lncRNA are presented relative to the healthy control group, as indicated by the horizontal dotted line at y=1, respectively. Statistical differences were analyzed using independent samples t -test. Bars indicate standard deviation. *P
Figure Legend Snippet: Differential expression patterns of placenta-related lncRNAs in PE plasma. Relative expression levels of NONHSAT116812 and NONHSAT145880 in late-onset PE group and control group 1 (n=52 per group) (A) and in early-onset PE group and control group 2 (n=58 per group) (B). 2 −ΔΔCq method was used to calculate lncRNA expression and the expression levels of each lncRNA are presented relative to the healthy control group, as indicated by the horizontal dotted line at y=1, respectively. Statistical differences were analyzed using independent samples t -test. Bars indicate standard deviation. *P

Techniques Used: Expressing, Standard Deviation

Sequencing results of plasma qPCR products of NONHSAT116812 (A) and NONHSAT145880 (B).
Figure Legend Snippet: Sequencing results of plasma qPCR products of NONHSAT116812 (A) and NONHSAT145880 (B).

Techniques Used: Sequencing, Real-time Polymerase Chain Reaction

16) Product Images from "Paternal Uniparental Disomy 11p15.5 in the Pancreatic Nodule of an Infant With Costello Syndrome: Shared Mechanism for Hyperinsulinemic Hypoglycemia in Neonates With Costello and Beckwith–Wiedemann Syndrome and Somatic Loss of Heterozygosity in Costello Syndrome Driving Clonal Expansion"

Article Title: Paternal Uniparental Disomy 11p15.5 in the Pancreatic Nodule of an Infant With Costello Syndrome: Shared Mechanism for Hyperinsulinemic Hypoglycemia in Neonates With Costello and Beckwith–Wiedemann Syndrome and Somatic Loss of Heterozygosity in Costello Syndrome Driving Clonal Expansion

Journal: American journal of medical genetics. Part A

doi: 10.1002/ajmg.a.37471

Diagram of UPD for chromosome 11 and of point mutations affecting either ABCC8 or HRAS ].
Figure Legend Snippet: Diagram of UPD for chromosome 11 and of point mutations affecting either ABCC8 or HRAS ].

Techniques Used:

17) Product Images from "Differential Detection of Avian Oncogenic Viruses in Poultry Layer Farms and Turkeys by Use of Multiplex PCR"

Article Title: Differential Detection of Avian Oncogenic Viruses in Poultry Layer Farms and Turkeys by Use of Multiplex PCR

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.00457-12

Specificity of multiplex PCR primers using cell culture-positive DNA. (Left) The meq gene primer amplicon (856 bp) was seen in MDV-positive cell culture DNA (lane 1) and not in ALV or REV (lanes 2 and 3). (Middle) The ALV p27 gene primer amplicon (613
Figure Legend Snippet: Specificity of multiplex PCR primers using cell culture-positive DNA. (Left) The meq gene primer amplicon (856 bp) was seen in MDV-positive cell culture DNA (lane 1) and not in ALV or REV (lanes 2 and 3). (Middle) The ALV p27 gene primer amplicon (613

Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Cell Culture, Amplification

Multiplex PCR amplification of tissue DNA. All the tissue samples show an amplicon size of 396 bp for the β- actin internal control, except the nontemplate control (lane 8). Lane 1, 1-kbp DNA ladder. Lane 2, ALV- and REV-positive tissue DNA showing
Figure Legend Snippet: Multiplex PCR amplification of tissue DNA. All the tissue samples show an amplicon size of 396 bp for the β- actin internal control, except the nontemplate control (lane 8). Lane 1, 1-kbp DNA ladder. Lane 2, ALV- and REV-positive tissue DNA showing

Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Amplification

Optimization of PCR using individual tissue DNA with individual multiplex PCR primers. Lanes: 1, 1-kb DNA ladder; 2, ALV-positive cell culture DNA showing an amplicon size of 613 bp with p27 gene primers; 3, MDV-positive cell culture DNA showing an amplicon
Figure Legend Snippet: Optimization of PCR using individual tissue DNA with individual multiplex PCR primers. Lanes: 1, 1-kb DNA ladder; 2, ALV-positive cell culture DNA showing an amplicon size of 613 bp with p27 gene primers; 3, MDV-positive cell culture DNA showing an amplicon

Techniques Used: Polymerase Chain Reaction, Multiplex Assay, Cell Culture, Amplification

Sensitivity of multiplex PCR primers using PCR product cloned TA plasmid DNA. (a) The meq gene primer amplicon (856 bp) was seen in plasmid copy numbers of 5 14 (lane 1) and up to 5 2 in serial dilution (lanes 3 to 14). (b) The ALV p27 gene primer amplicon
Figure Legend Snippet: Sensitivity of multiplex PCR primers using PCR product cloned TA plasmid DNA. (a) The meq gene primer amplicon (856 bp) was seen in plasmid copy numbers of 5 14 (lane 1) and up to 5 2 in serial dilution (lanes 3 to 14). (b) The ALV p27 gene primer amplicon

Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Clone Assay, Plasmid Preparation, Amplification, Serial Dilution

18) Product Images from "Differential Detection of Avian Oncogenic Viruses in Poultry Layer Farms and Turkeys by Use of Multiplex PCR"

Article Title: Differential Detection of Avian Oncogenic Viruses in Poultry Layer Farms and Turkeys by Use of Multiplex PCR

Journal: Journal of Clinical Microbiology

doi: 10.1128/JCM.00457-12

Specificity of multiplex PCR primers using cell culture-positive DNA. (Left) The meq gene primer amplicon (856 bp) was seen in MDV-positive cell culture DNA (lane 1) and not in ALV or REV (lanes 2 and 3). (Middle) The ALV p27 gene primer amplicon (613
Figure Legend Snippet: Specificity of multiplex PCR primers using cell culture-positive DNA. (Left) The meq gene primer amplicon (856 bp) was seen in MDV-positive cell culture DNA (lane 1) and not in ALV or REV (lanes 2 and 3). (Middle) The ALV p27 gene primer amplicon (613

Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Cell Culture, Amplification

Multiplex PCR amplification of tissue DNA. All the tissue samples show an amplicon size of 396 bp for the β- actin internal control, except the nontemplate control (lane 8). Lane 1, 1-kbp DNA ladder. Lane 2, ALV- and REV-positive tissue DNA showing
Figure Legend Snippet: Multiplex PCR amplification of tissue DNA. All the tissue samples show an amplicon size of 396 bp for the β- actin internal control, except the nontemplate control (lane 8). Lane 1, 1-kbp DNA ladder. Lane 2, ALV- and REV-positive tissue DNA showing

Techniques Used: Multiplex Assay, Polymerase Chain Reaction, Amplification

19) Product Images from "Immune monitoring and TCR sequencing of CD4 T cells in a long term responsive patient with metastasized pancreatic ductal carcinoma treated with individualized, neoepitope-derived multipeptide vaccines: a case report"

Article Title: Immune monitoring and TCR sequencing of CD4 T cells in a long term responsive patient with metastasized pancreatic ductal carcinoma treated with individualized, neoepitope-derived multipeptide vaccines: a case report

Journal: Journal of Translational Medicine

doi: 10.1186/s12967-018-1382-1

Complexity score of peripheral blood TCRVα and TCR-Vβ repertoire in our patient at the 1st, 2nd and 3rd immune monitoring as well as in healthy controls (HC). The complexity of Vβ- and Vα-chain repertoires was determined by counting the number of peaks in spectratype analysis. A score of 8 describes a normal CDR3 size variability of 8–10 peaks per Gaussian curve, a score of 1 refers to profiles showing single peak, 0 describes the absence of peaks. The overall TCR complexity (complexity score) is the sum of 26 individual TCR Vβ- or 34 TCRVα family scores respectively (with a maximum of 26 × 8 = 208 for the β-, and 34 × 8 = 272 for the Vα families)
Figure Legend Snippet: Complexity score of peripheral blood TCRVα and TCR-Vβ repertoire in our patient at the 1st, 2nd and 3rd immune monitoring as well as in healthy controls (HC). The complexity of Vβ- and Vα-chain repertoires was determined by counting the number of peaks in spectratype analysis. A score of 8 describes a normal CDR3 size variability of 8–10 peaks per Gaussian curve, a score of 1 refers to profiles showing single peak, 0 describes the absence of peaks. The overall TCR complexity (complexity score) is the sum of 26 individual TCR Vβ- or 34 TCRVα family scores respectively (with a maximum of 26 × 8 = 208 for the β-, and 34 × 8 = 272 for the Vα families)

Techniques Used:

20) Product Images from "Adaptor protein-2 sigma subunit mutations causing familial hypocalciuric hypercalcaemia type 3 (FHH3) demonstrate genotype–phenotype correlations, codon bias and dominant-negative effects"

Article Title: Adaptor protein-2 sigma subunit mutations causing familial hypocalciuric hypercalcaemia type 3 (FHH3) demonstrate genotype–phenotype correlations, codon bias and dominant-negative effects

Journal: Human Molecular Genetics

doi: 10.1093/hmg/ddv226

Detection of de novo AP2S1 mutations in families 02/03 and 06/13b. ( A ) DNA sequence analyses of the probands (arrowed) revealed a G-to-T transversion at codon 15, predicted to result in a missense amino acid substitution of Arg to Leu, and loss of a Hh aI restriction endonuclease site. ( B ) Restriction map showing that Hh aI digestion would result in two products of 143 and 252 bp from the wild-type (WT) sequence, but would not affect the mutant (m) sequence. PCR and Hh aI digestion revealed the probands [individual II.4 of family 02/03 ( C ) and individual II.1 of family 06/13b ( D )] to be heterozygous for the Arg15Leu mutation. The absence of the Arg15Leu mutation in the unaffected parents of both probands is consistent with the mutation arising de novo .
Figure Legend Snippet: Detection of de novo AP2S1 mutations in families 02/03 and 06/13b. ( A ) DNA sequence analyses of the probands (arrowed) revealed a G-to-T transversion at codon 15, predicted to result in a missense amino acid substitution of Arg to Leu, and loss of a Hh aI restriction endonuclease site. ( B ) Restriction map showing that Hh aI digestion would result in two products of 143 and 252 bp from the wild-type (WT) sequence, but would not affect the mutant (m) sequence. PCR and Hh aI digestion revealed the probands [individual II.4 of family 02/03 ( C ) and individual II.1 of family 06/13b ( D )] to be heterozygous for the Arg15Leu mutation. The absence of the Arg15Leu mutation in the unaffected parents of both probands is consistent with the mutation arising de novo .

Techniques Used: Sequencing, Mutagenesis, Polymerase Chain Reaction

21) Product Images from "Iron Corrosion Induced by Nonhydrogenotrophic Nitrate-Reducing Prolixibacter sp. Strain MIC1-1"

Article Title: Iron Corrosion Induced by Nonhydrogenotrophic Nitrate-Reducing Prolixibacter sp. Strain MIC1-1

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.03741-14

Phylogenetic tree of Prolixibacter sp. MIC1-1, related bacteria, and environmental clones based on the 16S rRNA gene sequences. The tree was inferred from an alignment of 1,308 bp of 16S rRNA gene sequences and constructed by NJ. The solid circles at
Figure Legend Snippet: Phylogenetic tree of Prolixibacter sp. MIC1-1, related bacteria, and environmental clones based on the 16S rRNA gene sequences. The tree was inferred from an alignment of 1,308 bp of 16S rRNA gene sequences and constructed by NJ. The solid circles at

Techniques Used: Clone Assay, Construct

22) Product Images from "Comprehensive Approaches to Molecular Biomarker Discovery for Detection and Identification of Cronobacter spp. (Enterobacter sakazakii) and Salmonella spp. ▿"

Article Title: Comprehensive Approaches to Molecular Biomarker Discovery for Detection and Identification of Cronobacter spp. (Enterobacter sakazakii) and Salmonella spp. ▿

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.02374-10

Phylogenetic analysis of the chitinase (A) and ompA (B) genes shows 2 distinct groups. Protein accession numbers correspond to GenBank.
Figure Legend Snippet: Phylogenetic analysis of the chitinase (A) and ompA (B) genes shows 2 distinct groups. Protein accession numbers correspond to GenBank.

Techniques Used:

Verification of analysis of chitinase and ompA genes as potential biomarkers.
Figure Legend Snippet: Verification of analysis of chitinase and ompA genes as potential biomarkers.

Techniques Used:

Agarose gel electrophoresis analysis of PCR products targeting the chitinase (2.2-kb) and ompA (469-bp) genes.
Figure Legend Snippet: Agarose gel electrophoresis analysis of PCR products targeting the chitinase (2.2-kb) and ompA (469-bp) genes.

Techniques Used: Agarose Gel Electrophoresis, Polymerase Chain Reaction

23) Product Images from "Two Genetic Determinants Acquired Late in Mus Evolution Regulate the Inclusion of Exon 5, which Alters Mouse APOBEC3 Translation Efficiency"

Article Title: Two Genetic Determinants Acquired Late in Mus Evolution Regulate the Inclusion of Exon 5, which Alters Mouse APOBEC3 Translation Efficiency

Journal: PLoS Pathogens

doi: 10.1371/journal.ppat.1002478

The effect of exon 5 and its downstream sequences on mA3 intron 5 splicing. (A) Distributions of sequence polymorphisms in the intron 5 of the Apobec3 gene locus between the B6 allele [NT_039621] and the Celera database sequence of mixed mouse DNA [NW_001030577.1]. Shorter horizontal lines below the thick one representing intron 5 indicate regions of sequenced BALB/c genome [DDBJ accession No. AB646261-AB646265], which show nucleotide sequences identical to corresponding Celera database sequences. Spans of the analyzed regions are 1–620, 661–1597, 1643–2058, 2759–3443, and 5558–6247 in base numbers starting from the first nucleotide of intron 5. SNP are shown with vertical lines, single-base indels with arrows, and deletions of ≥2 bases with triangles. Indels and deletions above the thick horizontal line that represents intron 5 are deletions in the B6 allele relative to the Celera sequence, while those underneath the horizontal line are deletions in the Celera sequence relative to the B6 allele sequence. (B) Plasmid constructions for the splicing assays. The exon 5–6 plasmids harbored either the B6 or BALB/c genomic fragment encompassing exons 5 and 6, including the entire intron 5 of the corresponding allele. Each of the remaining plasmids possessed a sequentially reduced length of the intron 5 as indicated. The precise size of each PCR-generated 5′ fragment included was as follows: 3177bp and 3185bp for B6 and BALB/c intron 5-Δ3′; 2106bp and 2086bp for B6 and BALB/c 200bp intron 5; 1120bp and 1110bp for B6 and BALB/c 1100bp intron 5; and 634bp and 620bp for B6 and BALB/c 600bp intron 5, respectively. The primers g–h are the same as shown in Figure 4 . (C) RT-PCR detection of spliced messages expressed from the B6 and BALB/c exon 5–6 plasmids along with those from the exon 4–7 plasmids as controls. Primers g and h were used. A lack of expression of the spliced message in cells transfected with the B6 exon 5–6 plasmid was evident. (D and F) Splicing assays using intron 5 deletion plasmids. The intron 5 fragment included in each plasmid is shown in (B). RT-PCR assays were performed with primers g and h. A portion of the transfected cells were utilized for luciferase assays to compare transfection efficiencies among the samples as shown in (C). Comparable levels of luciferase activities were observed in all samples in each experiment (data not shown). Quantitative real-time PCR data show averages of three reaction wells and SD. (E) Reciprocal chimeras were produced between B6 and BALB/c exon 5–6 by exchanging the cloned genomic DNA fragment at position 1100 within intron 5. The exact location of the above position 1100 for B6 and BALB/c intron 5 is described in the legend for (B). RT-PCR detection of spliced messages was performed with primers g and h. A portion of the transfected cells were utilized for luciferase assays to compare transfection efficiencies.
Figure Legend Snippet: The effect of exon 5 and its downstream sequences on mA3 intron 5 splicing. (A) Distributions of sequence polymorphisms in the intron 5 of the Apobec3 gene locus between the B6 allele [NT_039621] and the Celera database sequence of mixed mouse DNA [NW_001030577.1]. Shorter horizontal lines below the thick one representing intron 5 indicate regions of sequenced BALB/c genome [DDBJ accession No. AB646261-AB646265], which show nucleotide sequences identical to corresponding Celera database sequences. Spans of the analyzed regions are 1–620, 661–1597, 1643–2058, 2759–3443, and 5558–6247 in base numbers starting from the first nucleotide of intron 5. SNP are shown with vertical lines, single-base indels with arrows, and deletions of ≥2 bases with triangles. Indels and deletions above the thick horizontal line that represents intron 5 are deletions in the B6 allele relative to the Celera sequence, while those underneath the horizontal line are deletions in the Celera sequence relative to the B6 allele sequence. (B) Plasmid constructions for the splicing assays. The exon 5–6 plasmids harbored either the B6 or BALB/c genomic fragment encompassing exons 5 and 6, including the entire intron 5 of the corresponding allele. Each of the remaining plasmids possessed a sequentially reduced length of the intron 5 as indicated. The precise size of each PCR-generated 5′ fragment included was as follows: 3177bp and 3185bp for B6 and BALB/c intron 5-Δ3′; 2106bp and 2086bp for B6 and BALB/c 200bp intron 5; 1120bp and 1110bp for B6 and BALB/c 1100bp intron 5; and 634bp and 620bp for B6 and BALB/c 600bp intron 5, respectively. The primers g–h are the same as shown in Figure 4 . (C) RT-PCR detection of spliced messages expressed from the B6 and BALB/c exon 5–6 plasmids along with those from the exon 4–7 plasmids as controls. Primers g and h were used. A lack of expression of the spliced message in cells transfected with the B6 exon 5–6 plasmid was evident. (D and F) Splicing assays using intron 5 deletion plasmids. The intron 5 fragment included in each plasmid is shown in (B). RT-PCR assays were performed with primers g and h. A portion of the transfected cells were utilized for luciferase assays to compare transfection efficiencies among the samples as shown in (C). Comparable levels of luciferase activities were observed in all samples in each experiment (data not shown). Quantitative real-time PCR data show averages of three reaction wells and SD. (E) Reciprocal chimeras were produced between B6 and BALB/c exon 5–6 by exchanging the cloned genomic DNA fragment at position 1100 within intron 5. The exact location of the above position 1100 for B6 and BALB/c intron 5 is described in the legend for (B). RT-PCR detection of spliced messages was performed with primers g and h. A portion of the transfected cells were utilized for luciferase assays to compare transfection efficiencies.

Techniques Used: Sequencing, Plasmid Preparation, Polymerase Chain Reaction, Generated, Reverse Transcription Polymerase Chain Reaction, Expressing, Transfection, Luciferase, Real-time Polymerase Chain Reaction, Produced, Clone Assay

24) Product Images from "CDH1 Missense Variant c.1679C>G (p.T560R) Completely Disrupts Normal Splicing through Creation of a Novel 5’ Splice Site"

Article Title: CDH1 Missense Variant c.1679C>G (p.T560R) Completely Disrupts Normal Splicing through Creation of a Novel 5’ Splice Site

Journal: PLoS ONE

doi: 10.1371/journal.pone.0165654

Semi-quantitative fragment analysis of  CDH1  RNA transcripts. (A) RT-PCR fragments generated from  CDH1  spanning exons 10–12 cDNAs from patient, patient’s brother, and eight controls (results from one representative fragment analysis run were shown) were analyzed by capillary electrophoresis (3730 Genetic Analyzer). The three peaks observed (from left to right) are: del Exon 11, del 32nt, and Full length. (B) Quantification of the three transcripts in controls and affected patients (the proband and his brother). The peak heights for the three transcripts in the patient and patient’s brother were averaged because the ratios are similar. The peak heights for the eight control samples were also averaged. Blue, red and green bars represent percentages of fragments with exon 11deletion, a deletion of 32 nucleotides within exon 11, and wild type fragments. Error bars represent standard error in comparing controls and patients for each fragment. Asterisks represent statistical significance between controls and patients.
Figure Legend Snippet: Semi-quantitative fragment analysis of CDH1 RNA transcripts. (A) RT-PCR fragments generated from CDH1 spanning exons 10–12 cDNAs from patient, patient’s brother, and eight controls (results from one representative fragment analysis run were shown) were analyzed by capillary electrophoresis (3730 Genetic Analyzer). The three peaks observed (from left to right) are: del Exon 11, del 32nt, and Full length. (B) Quantification of the three transcripts in controls and affected patients (the proband and his brother). The peak heights for the three transcripts in the patient and patient’s brother were averaged because the ratios are similar. The peak heights for the eight control samples were also averaged. Blue, red and green bars represent percentages of fragments with exon 11deletion, a deletion of 32 nucleotides within exon 11, and wild type fragments. Error bars represent standard error in comparing controls and patients for each fragment. Asterisks represent statistical significance between controls and patients.

Techniques Used: Reverse Transcription Polymerase Chain Reaction, Generated, Electrophoresis

25) Product Images from "Novel 4-bp Intronic Deletion (c.1560+3_1560+6del) in LEMD3 in a Korean Patient With Osteopoikilosis"

Article Title: Novel 4-bp Intronic Deletion (c.1560+3_1560+6del) in LEMD3 in a Korean Patient With Osteopoikilosis

Journal: Annals of Laboratory Medicine

doi: 10.3343/alm.2017.37.6.540

Novel splice site variant in the LEMD3 gene. (A) Sequencing pattern of LEMD3 shows overlapping peaks due to a heterozygous variant in intron 2 (c.1560+3_1560+6del; arrow). (B) Cloning of reverse transcription (RT)-PCR products reveals two clones: a normal clone and an abnormal clone without exon 2. (C) Schematic illustration of aberrant splicing due to the heterozygous 4-bp deletion.
Figure Legend Snippet: Novel splice site variant in the LEMD3 gene. (A) Sequencing pattern of LEMD3 shows overlapping peaks due to a heterozygous variant in intron 2 (c.1560+3_1560+6del; arrow). (B) Cloning of reverse transcription (RT)-PCR products reveals two clones: a normal clone and an abnormal clone without exon 2. (C) Schematic illustration of aberrant splicing due to the heterozygous 4-bp deletion.

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

26) Product Images from "Analysis of the gut microbiota of walking sticks (Phasmatodea)"

Article Title: Analysis of the gut microbiota of walking sticks (Phasmatodea)

Journal: BMC Research Notes

doi: 10.1186/1756-0500-6-368

Principal Coordinate Analyses (PCoA) of the microbiota. The samples are color-coded by type: blue squares, P . schultei anterior midgut (Ps_AMG) samples; green circles, R . artemis anterior midgut (Ra_AMG) samples; red triangles, R . artemis posterior midgut (Ra_PMG) samples. The label indicates the individual id within each species. The numbers in parentheses in axis labels indicate the percentage of variance explained. (A) All 5,679 bacterial 16S rDNA reads. (B) Excluding Spiroplasma reads.
Figure Legend Snippet: Principal Coordinate Analyses (PCoA) of the microbiota. The samples are color-coded by type: blue squares, P . schultei anterior midgut (Ps_AMG) samples; green circles, R . artemis anterior midgut (Ra_AMG) samples; red triangles, R . artemis posterior midgut (Ra_PMG) samples. The label indicates the individual id within each species. The numbers in parentheses in axis labels indicate the percentage of variance explained. (A) All 5,679 bacterial 16S rDNA reads. (B) Excluding Spiroplasma reads.

Techniques Used:

Relative abundances of reads of the different phyla. (A) All 5,679 bacterial 16S rDNA reads. (B) Excluding Spiroplasma reads.
Figure Legend Snippet: Relative abundances of reads of the different phyla. (A) All 5,679 bacterial 16S rDNA reads. (B) Excluding Spiroplasma reads.

Techniques Used:

27) Product Images from "Novel physiological RECQL4 alternative transcript disclosed by molecular characterisation of Rothmund–Thomson Syndrome sibs with mild phenotype"

Article Title: Novel physiological RECQL4 alternative transcript disclosed by molecular characterisation of Rothmund–Thomson Syndrome sibs with mild phenotype

Journal: European Journal of Human Genetics

doi: 10.1038/ejhg.2014.18

Real-time expression profile of RECQL4 isoforms. ( a ) RECQL4 partially skipped exon 14 and ( b ) RECQL4 with different RECQL4 mutations compared with five controls
Figure Legend Snippet: Real-time expression profile of RECQL4 isoforms. ( a ) RECQL4 partially skipped exon 14 and ( b ) RECQL4 with different RECQL4 mutations compared with five controls

Techniques Used: Expressing

DNA and RNA characterisation of RECQL4 mutations in the index family. ( a ) Pedigree of the family with two siblings with Rothmund–Thomson syndrome (filled diamond) found to be compound heterozygotes for the paternal c.2272C > T and the maternal
Figure Legend Snippet: DNA and RNA characterisation of RECQL4 mutations in the index family. ( a ) Pedigree of the family with two siblings with Rothmund–Thomson syndrome (filled diamond) found to be compound heterozygotes for the paternal c.2272C > T and the maternal

Techniques Used:

28) Product Images from "Molecular Architecture of Muscles in an Acoel and Its Evolutionary Implications"

Article Title: Molecular Architecture of Muscles in an Acoel and Its Evolutionary Implications

Journal: Journal of experimental zoology. Part B, Molecular and developmental evolution

doi: 10.1002/jez.b.21416

SrAct , SrTnI , and SrTrp gene expression patterns in the acoel Symsagittifera roscoffensis . Anterior is toward the left in all aspects. (A) SrAct expression in a juvenile. The positive cells appear scattered along the AP axis of the juvenile. The highest
Figure Legend Snippet: SrAct , SrTnI , and SrTrp gene expression patterns in the acoel Symsagittifera roscoffensis . Anterior is toward the left in all aspects. (A) SrAct expression in a juvenile. The positive cells appear scattered along the AP axis of the juvenile. The highest

Techniques Used: Expressing

29) Product Images from "Intrinsic Replication Competences of HIV Strains After Zidovudine/Lamivudine/Nevirapine Treatment in the Philippines"

Article Title: Intrinsic Replication Competences of HIV Strains After Zidovudine/Lamivudine/Nevirapine Treatment in the Philippines

Journal: Journal of the International Association of Providers of AIDS Care

doi: 10.1177/2325958219856579

Relationship between plasma HIV loads and replication potencies of HIV strains. A correlation analysis was performed between plasma HIV loads and the amounts of HIV produced from peripheral blood mononuclear cells inoculated with HIV (HIV-RNA: 10 6 copies/1.5 × 10 6 cells/mL) in 7 days (n = 37). Pearson correlation coefficient ( r ) was 0.375 ( P
Figure Legend Snippet: Relationship between plasma HIV loads and replication potencies of HIV strains. A correlation analysis was performed between plasma HIV loads and the amounts of HIV produced from peripheral blood mononuclear cells inoculated with HIV (HIV-RNA: 10 6 copies/1.5 × 10 6 cells/mL) in 7 days (n = 37). Pearson correlation coefficient ( r ) was 0.375 ( P

Techniques Used: Produced

30) Product Images from "Genotype determination of the OPN1LW/OPN1MW genes: novel disease-causing mechanisms in Japanese patients with blue cone monochromacy"

Article Title: Genotype determination of the OPN1LW/OPN1MW genes: novel disease-causing mechanisms in Japanese patients with blue cone monochromacy

Journal: Scientific Reports

doi: 10.1038/s41598-018-29891-9

Genotype of Case 4. ( A ) Overview of the genotype of Case 4. Case 4 had a large deletion of 23,389 bp including exons 2–6 of the first gene. The intact LCR and second gene were present. The second gene had exons 2–5 of M type and exon 3 with LVVVA haplotype. ( B ) Upper row shows the consensus sequence for the left monomer of the  Alu  element (complementary sequence of AluSx). Middle row shows a part of intron 1 of the first gene (the number is from the 5′ splice site of intron 1). Lower row shows a part of the intergenic region (the number is from the stop codon in exon 6 of the first gene). The nucleotides differing among the regions are shown in red and by asterisks. The actual sequence obtained in Case 4 is underlined. ( C ) Partial sequence data around the breakpoint of the deletion. The breakpoint is somewhere in the common 6-bp sequence.
Figure Legend Snippet: Genotype of Case 4. ( A ) Overview of the genotype of Case 4. Case 4 had a large deletion of 23,389 bp including exons 2–6 of the first gene. The intact LCR and second gene were present. The second gene had exons 2–5 of M type and exon 3 with LVVVA haplotype. ( B ) Upper row shows the consensus sequence for the left monomer of the Alu element (complementary sequence of AluSx). Middle row shows a part of intron 1 of the first gene (the number is from the 5′ splice site of intron 1). Lower row shows a part of the intergenic region (the number is from the stop codon in exon 6 of the first gene). The nucleotides differing among the regions are shown in red and by asterisks. The actual sequence obtained in Case 4 is underlined. ( C ) Partial sequence data around the breakpoint of the deletion. The breakpoint is somewhere in the common 6-bp sequence.

Techniques Used: Sequencing

31) Product Images from "Molecular Characterization of Multidrug-Resistant Mycobacterium tuberculosis Isolated in Nepal"

Article Title: Molecular Characterization of Multidrug-Resistant Mycobacterium tuberculosis Isolated in Nepal

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.06418-11

Sequencing of the rpoB and katG encoding regions and the inhA promoter region.
Figure Legend Snippet: Sequencing of the rpoB and katG encoding regions and the inhA promoter region.

Techniques Used: Sequencing

32) Product Images from "Molecular identification of a major quantitative trait locus, qLTG3–1, controlling low-temperature germinability in rice"

Article Title: Molecular identification of a major quantitative trait locus, qLTG3–1, controlling low-temperature germinability in rice

Journal:

doi: 10.1073/pnas.0805303105

Expression of qLTG3–1 . Northern blot analysis was used to measure the qLTG3–1 expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was
Figure Legend Snippet: Expression of qLTG3–1 . Northern blot analysis was used to measure the qLTG3–1 expression levels in total RNA extracted from different tissues of Hayamasari (HY), the NIL (NIL), and Italica Livorno (IL). Ethidium bromide stained rRNA was

Techniques Used: Expressing, Northern Blot, Staining

Introductions of the functional qLTG3–1 gene from Italica Livorno into Hayamasari. The germination of homozygous transformants obtained by Agrobacterium -mediated transformation of Hayamasari with the genomic fragment of qLTG3–1 ( A ) and
Figure Legend Snippet: Introductions of the functional qLTG3–1 gene from Italica Livorno into Hayamasari. The germination of homozygous transformants obtained by Agrobacterium -mediated transformation of Hayamasari with the genomic fragment of qLTG3–1 ( A ) and

Techniques Used: Functional Assay, Transformation Assay

33) Product Images from "Functional characterization of the first missense variant in CEP78, a founder allele associated with cone‐rod dystrophy, hearing loss, and reduced male fertility, et al. Functional characterization of the first missense variant in CEP78, a founder allele associated with cone‐rod dystrophy, hearing loss, and reduced male fertility"

Article Title: Functional characterization of the first missense variant in CEP78, a founder allele associated with cone‐rod dystrophy, hearing loss, and reduced male fertility, et al. Functional characterization of the first missense variant in CEP78, a founder allele associated with cone‐rod dystrophy, hearing loss, and reduced male fertility

Journal: Human Mutation

doi: 10.1002/humu.23993

Location of known CEP78 variants. Schematic diagram of the CEP78 protein showing the location of the previously described truncating variants and the novel variants reported in this study (in bold). The previously published variant causing RP is indicated with a dashed line. CEP78 includes multiple leucine‐rich repeats (LRR, in gray) located at the N‐terminal, and a coiled‐coil domain at the C‐terminal (in black). The missense change described in this study is located in one of the LRRs. The splice site substitution is predicted to cause skipping of exon 13. This figure has been adapted from material from Brunk et al. ( 2016 ). RP, retinitis pigmentosa
Figure Legend Snippet: Location of known CEP78 variants. Schematic diagram of the CEP78 protein showing the location of the previously described truncating variants and the novel variants reported in this study (in bold). The previously published variant causing RP is indicated with a dashed line. CEP78 includes multiple leucine‐rich repeats (LRR, in gray) located at the N‐terminal, and a coiled‐coil domain at the C‐terminal (in black). The missense change described in this study is located in one of the LRRs. The splice site substitution is predicted to cause skipping of exon 13. This figure has been adapted from material from Brunk et al. ( 2016 ). RP, retinitis pigmentosa

Techniques Used: Variant Assay

34) Product Images from "Efficient transposition of the Tol2 transposable element from a single-copy donor in zebrafish"

Article Title: Efficient transposition of the Tol2 transposable element from a single-copy donor in zebrafish

Journal:

doi: 10.1073/pnas.0810380105

Mobilization of Tol2 insertions by microinjection of transposase mRNA. ( A ) The structures of the XIG8A and SAGp22A insertions. Arrows indicate directions of genes. Arrowheads indicate primers used to detect excision. ( B ) A scheme for mobilization of
Figure Legend Snippet: Mobilization of Tol2 insertions by microinjection of transposase mRNA. ( A ) The structures of the XIG8A and SAGp22A insertions. Arrows indicate directions of genes. Arrowheads indicate primers used to detect excision. ( B ) A scheme for mobilization of

Techniques Used:

35) Product Images from "Impact of Preexisting Hepatitis C Virus Genotype 6 NS3, NS5A, and NS5B Polymorphisms on the In Vitro Potency of Direct-Acting Antiviral Agents"

Article Title: Impact of Preexisting Hepatitis C Virus Genotype 6 NS3, NS5A, and NS5B Polymorphisms on the In Vitro Potency of Direct-Acting Antiviral Agents

Journal: Antimicrobial Agents and Chemotherapy

doi: 10.1128/AAC.02205-18

In vitro susceptibility of HCV GT-6 NS5A RASs.
Figure Legend Snippet: In vitro susceptibility of HCV GT-6 NS5A RASs.

Techniques Used: In Vitro

HCV GT-6 NS5A resistance-associated substitutions by HCV GT-6 subtype.
Figure Legend Snippet: HCV GT-6 NS5A resistance-associated substitutions by HCV GT-6 subtype.

Techniques Used:

36) Product Images from "Experimental infection and transmission of Leishmania by Lutzomyia cruzi (Diptera: Psychodidae): Aspects of the ecology of parasite-vector interactions"

Article Title: Experimental infection and transmission of Leishmania by Lutzomyia cruzi (Diptera: Psychodidae): Aspects of the ecology of parasite-vector interactions

Journal: PLoS Neglected Tropical Diseases

doi: 10.1371/journal.pntd.0005401

Digestion of amplified products of the ITS1 region of Leishmania with the Hae III restriction enzyme. 1: 100-bp ladder marker; 2: negative control; 3–10: sand flies fed on hamsters infected with L . amazonensis ; 11–14: sand flies fed on dogs infected with L . infantum ; 15: positive control L . amazonensis (IFLA/BR/1967/PH8); 16: positive control L . infantum (MHOM/BR/1972/BH46); 17: sample not digested by Hae III; 18: 100-bp ladder marker.
Figure Legend Snippet: Digestion of amplified products of the ITS1 region of Leishmania with the Hae III restriction enzyme. 1: 100-bp ladder marker; 2: negative control; 3–10: sand flies fed on hamsters infected with L . amazonensis ; 11–14: sand flies fed on dogs infected with L . infantum ; 15: positive control L . amazonensis (IFLA/BR/1967/PH8); 16: positive control L . infantum (MHOM/BR/1972/BH46); 17: sample not digested by Hae III; 18: 100-bp ladder marker.

Techniques Used: Amplification, Marker, Negative Control, Infection, Positive Control

37) Product Images from "JAK3 mutations in Italian patients affected by SCID: New molecular aspects of a long‐known gene, et al. JAK3 mutations in Italian patients affected by SCID: New molecular aspects of a long‐known gene"

Article Title: JAK3 mutations in Italian patients affected by SCID: New molecular aspects of a long‐known gene, et al. JAK3 mutations in Italian patients affected by SCID: New molecular aspects of a long‐known gene

Journal: Molecular Genetics & Genomic Medicine

doi: 10.1002/mgg3.391

Characterization of JAK 3‐Pt4. (a) Genealogical tree and JAK 3 protein expression of Pt4. (b) The sequence alignment of the patient's BAM file on IGV (Integrative Genomics Viewer) revealed the indicated mutations confirmed by Sanger. (c) Phospho‐ STAT 5 ( pSTAT 5) evaluated in response to IL 2 or IL 15 stimulation in patients’ EBV ‐B cells compared with HD
Figure Legend Snippet: Characterization of JAK 3‐Pt4. (a) Genealogical tree and JAK 3 protein expression of Pt4. (b) The sequence alignment of the patient's BAM file on IGV (Integrative Genomics Viewer) revealed the indicated mutations confirmed by Sanger. (c) Phospho‐ STAT 5 ( pSTAT 5) evaluated in response to IL 2 or IL 15 stimulation in patients’ EBV ‐B cells compared with HD

Techniques Used: Expressing, Sequencing

38) Product Images from "Molecular identification and characterization of Sarcocystis spp. in horsemeat and beef marketed in Japan"

Article Title: Molecular identification and characterization of Sarcocystis spp. in horsemeat and beef marketed in Japan

Journal: Parasite

doi: 10.1051/parasite/2018026

Phylogenetic relationships obtained by maximum likelihood (ML) analysis of Sarcocystis 18S rRNA (A) and mtDNA cox1 (B) gene sequences. ML trees were derived using a general time-reversible model employing estimates of the proportion of invariable sites and the Gamma distribution. Significant bootstrap support ( > 50%) from 1,000 replicates of the ML and the maximum parsimony (MP) method are shown above each node in the order ML/MP. Support for a node of less than 50% is indicated by an asterisk. Underlined samples are those sequenced in this study. The scale bar represents the distance in substitutions per nucleotide. GenBank accession numbers are shown in parentheses.
Figure Legend Snippet: Phylogenetic relationships obtained by maximum likelihood (ML) analysis of Sarcocystis 18S rRNA (A) and mtDNA cox1 (B) gene sequences. ML trees were derived using a general time-reversible model employing estimates of the proportion of invariable sites and the Gamma distribution. Significant bootstrap support ( > 50%) from 1,000 replicates of the ML and the maximum parsimony (MP) method are shown above each node in the order ML/MP. Support for a node of less than 50% is indicated by an asterisk. Underlined samples are those sequenced in this study. The scale bar represents the distance in substitutions per nucleotide. GenBank accession numbers are shown in parentheses.

Techniques Used: Derivative Assay

39) Product Images from "Limb-girdle muscular dystrophy 1F is caused by a microdeletion in the transportin 3 gene"

Article Title: Limb-girdle muscular dystrophy 1F is caused by a microdeletion in the transportin 3 gene

Journal: Brain

doi: 10.1093/brain/awt074

Effects of the c.2771del mutation on TNPO3 messenger RNA and protein. ( A ) The 3’-terminal coding and untranslated region (UTR) sequences of TNPO3 transcripts, including the 3’-end of the exon 23 (black font) and the 5’-end of the
Figure Legend Snippet: Effects of the c.2771del mutation on TNPO3 messenger RNA and protein. ( A ) The 3’-terminal coding and untranslated region (UTR) sequences of TNPO3 transcripts, including the 3’-end of the exon 23 (black font) and the 5’-end of the

Techniques Used: Mutagenesis

Anti-TNPO3 and DAPI staining of muscle from affected individuals and controls. Immunofluorescence-stained muscle from two affected individuals (Subject IV-36: A–C , Subject V-14: D–F ) and two control subjects (one not shown) ( G–I
Figure Legend Snippet: Anti-TNPO3 and DAPI staining of muscle from affected individuals and controls. Immunofluorescence-stained muscle from two affected individuals (Subject IV-36: A–C , Subject V-14: D–F ) and two control subjects (one not shown) ( G–I

Techniques Used: Staining, Immunofluorescence

40) Product Images from "SNAIL is a key regulator of alveolar rhabdomyosarcoma tumor growth and differentiation through repression of MYF5 and MYOD function"

Article Title: SNAIL is a key regulator of alveolar rhabdomyosarcoma tumor growth and differentiation through repression of MYF5 and MYOD function

Journal: Cell Death & Disease

doi: 10.1038/s41419-018-0693-8

SNAIL is a direct transcriptional repressor of MYF5 expression and regulator of MYOD activity. a SNAIL silencing in RH30 cells induces MYOD binding to GC rich E-Box sequences. Nuclear protein extracts from both undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium supplemented with 2% HS were used in TransAM MyoD DNA-binding ELISA. To monitor the specificity of the assay, the wild-type consensus oligonucleotide (wt) and mutated (mut) sequences were used as competitors for MYOD binding from cell extracts; n = 3. b SNAIL binds to the MYF5 and E-cadherin promoters in RH30 cells. The promoter of MYF5 (~1000 bb) was screened for putative SNAIL transcription factor binding sites and the results were validated by Chip Assay. The images depict one representative result of the ChIP assay. Proteins bound to DNA were immunoprecipitated with the anti-SNAIL antibody, negative IgG control, positive histone H3 control and input DNA control was analyzed. Fragments of the MYF5 and E-cadherin promoters were amplified by PCR and visualized on agarose gels stained with ethidium bromide. c SNAIL silencing by siRNA in RH30 WT cells induces MYF5 promoter activation and luciferase expression when cells are transfected with MYF5@pNL plasmid (luciferase under control with MYF5 promoter), whereas MYOD silencing by siRNA does not exert any effect. SNAIL and MYOD compete for binding to MYF5 promoter in RH30 shSNAIL cells ( d ), RH41 WT ( e ), and RH41 shSNAIL cells ( f ), when cells are transfected with MYF5@pNL plasmid and siRNA against SNAIL, MYOD or siSCR (scrambled siRNA). The data were normalized to mCherry fluorescence level in each well. pNL (luciferase plasmid without promoter) served as a negative control and Ubc@pNL plasmid (luciferase under control of ubiquitin C promoter) was a positive control. The data represent the mean ± SEM or are representative images of at least 3 independent experiments. * p
Figure Legend Snippet: SNAIL is a direct transcriptional repressor of MYF5 expression and regulator of MYOD activity. a SNAIL silencing in RH30 cells induces MYOD binding to GC rich E-Box sequences. Nuclear protein extracts from both undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium supplemented with 2% HS were used in TransAM MyoD DNA-binding ELISA. To monitor the specificity of the assay, the wild-type consensus oligonucleotide (wt) and mutated (mut) sequences were used as competitors for MYOD binding from cell extracts; n = 3. b SNAIL binds to the MYF5 and E-cadherin promoters in RH30 cells. The promoter of MYF5 (~1000 bb) was screened for putative SNAIL transcription factor binding sites and the results were validated by Chip Assay. The images depict one representative result of the ChIP assay. Proteins bound to DNA were immunoprecipitated with the anti-SNAIL antibody, negative IgG control, positive histone H3 control and input DNA control was analyzed. Fragments of the MYF5 and E-cadherin promoters were amplified by PCR and visualized on agarose gels stained with ethidium bromide. c SNAIL silencing by siRNA in RH30 WT cells induces MYF5 promoter activation and luciferase expression when cells are transfected with MYF5@pNL plasmid (luciferase under control with MYF5 promoter), whereas MYOD silencing by siRNA does not exert any effect. SNAIL and MYOD compete for binding to MYF5 promoter in RH30 shSNAIL cells ( d ), RH41 WT ( e ), and RH41 shSNAIL cells ( f ), when cells are transfected with MYF5@pNL plasmid and siRNA against SNAIL, MYOD or siSCR (scrambled siRNA). The data were normalized to mCherry fluorescence level in each well. pNL (luciferase plasmid without promoter) served as a negative control and Ubc@pNL plasmid (luciferase under control of ubiquitin C promoter) was a positive control. The data represent the mean ± SEM or are representative images of at least 3 independent experiments. * p

Techniques Used: Expressing, Activity Assay, Binding Assay, Enzyme-linked Immunosorbent Assay, Chromatin Immunoprecipitation, Immunoprecipitation, Amplification, Polymerase Chain Reaction, Staining, Activation Assay, Luciferase, Transfection, Plasmid Preparation, Fluorescence, Negative Control, Positive Control

SNAIL expression is associated with RMS subtype and myogenic differentiation. a Expression of early and late myogenic factors in 158 RMS samples was estimated previously by microarray and deposited in GEO database with accession number: GSE92689 (ref. 20 ). SNAIL level negatively correlates with MYF5 level in RMS (Pearson correlation). b SNAIL level positively correlates with MYOD level in RMS (Pearson correlation). R—Pearson correlation coefficient; p—significance value ( c ) Increased SNAIL levels in RMS stage 2,3 and 4 compared to 1 were demonstrated in a group of 158 RMS samples (microarray data, GEO database GSE92689). The data are presented as Whisker plots min to max. d Increased SNAIL level in ARMS compared to ERMS was demonstrated in a group of 158 RMS samples (microarray data, GEO database GSE92689). The data are presented as Whisker plots min to max. e SNAIL expression was quantified by qPCR using the ΔCt quantification method and GAPDH as a housekeeping gene control in ARMS and ERMS cell lines and human primary myoblasts. The SNAIL level is increased in RH30 and RH41 ARMS cell lines compared to RD and RH18 ERMS cell lines, and the level is comparable with the SNAIL level in myoblasts at the early passage (undiff.), whereas in the differentiated myotubes (diff.) SNAIL level is more comparable with ERMS; n = 3. f Differentiation of RH30 cells by culture in medium supplemented with 2% HS for 7 days downregulates SNAIL expression at the mRNA level (qPCR) and protein level (Western blotting); n = 4. The data represent the mean ± SEM. * p
Figure Legend Snippet: SNAIL expression is associated with RMS subtype and myogenic differentiation. a Expression of early and late myogenic factors in 158 RMS samples was estimated previously by microarray and deposited in GEO database with accession number: GSE92689 (ref. 20 ). SNAIL level negatively correlates with MYF5 level in RMS (Pearson correlation). b SNAIL level positively correlates with MYOD level in RMS (Pearson correlation). R—Pearson correlation coefficient; p—significance value ( c ) Increased SNAIL levels in RMS stage 2,3 and 4 compared to 1 were demonstrated in a group of 158 RMS samples (microarray data, GEO database GSE92689). The data are presented as Whisker plots min to max. d Increased SNAIL level in ARMS compared to ERMS was demonstrated in a group of 158 RMS samples (microarray data, GEO database GSE92689). The data are presented as Whisker plots min to max. e SNAIL expression was quantified by qPCR using the ΔCt quantification method and GAPDH as a housekeeping gene control in ARMS and ERMS cell lines and human primary myoblasts. The SNAIL level is increased in RH30 and RH41 ARMS cell lines compared to RD and RH18 ERMS cell lines, and the level is comparable with the SNAIL level in myoblasts at the early passage (undiff.), whereas in the differentiated myotubes (diff.) SNAIL level is more comparable with ERMS; n = 3. f Differentiation of RH30 cells by culture in medium supplemented with 2% HS for 7 days downregulates SNAIL expression at the mRNA level (qPCR) and protein level (Western blotting); n = 4. The data represent the mean ± SEM. * p

Techniques Used: Expressing, Microarray, Whisker Assay, Real-time Polymerase Chain Reaction, Western Blot

SNAIL silencing in ARMS cells induces a spindle-shaped phenotype and inhibits proliferation. a SNAIL silencing by siRNA induces the acquisition of spindle-shaped phenotype of RH41 and RH30 cells and diminishes their proliferation. RH30 ARMS cells were transfected with siRNA against SNAIL (siSNAIL) and a scrambled siRNA sequence (siRNA). 24 h after transfection medium was changed for a differentiating medium containing 2% HS for the next 2 days. SNAIL silencing with siRNA for 3 days was validated by qPCR; n = 4. The morphology of the cells was visualized with Wright’s staining (error bar represent 100 μm). Proliferation was evaluated by MTS assay; n = 3. b To stably silence the SNAIL level, RH30 cells were transduced with shRNA lentiviral vectors targeting SNAIL (shSNAIL) and control vectors (shCTRL), and these cells were selected with puromycin. SNAIL silencing was validated by qPCR ( n = 3) and Western blotting (total cell extracts). c Stable SNAIL silencing in RH30 cells leads to the acquisition of a spindle- shaped phenotype and reorganization of the cytoskeleton. The morphology of RH30 cells differentiated for 4 days was visualized with Wright’s staining and for 6 days with phase contrast microscopy. d SNAIL silencing and the differentiation of RH30 cells led to cell cycle arrest at the G0-G1 phase and diminished percentage of the cells in S phase. RH30 cells were differentiated for 7 days in medium containing 2% HS. Subsequently, the cell cycle and BrdU incorporation in S phase were analyzed by flow cytometry—the cells were stained with anti-BrdU antibody conjugated with APC and with 7AAD. The data in the graphs represent the mean ± SEM or are representative images of at least 3 independent experiments. * p
Figure Legend Snippet: SNAIL silencing in ARMS cells induces a spindle-shaped phenotype and inhibits proliferation. a SNAIL silencing by siRNA induces the acquisition of spindle-shaped phenotype of RH41 and RH30 cells and diminishes their proliferation. RH30 ARMS cells were transfected with siRNA against SNAIL (siSNAIL) and a scrambled siRNA sequence (siRNA). 24 h after transfection medium was changed for a differentiating medium containing 2% HS for the next 2 days. SNAIL silencing with siRNA for 3 days was validated by qPCR; n = 4. The morphology of the cells was visualized with Wright’s staining (error bar represent 100 μm). Proliferation was evaluated by MTS assay; n = 3. b To stably silence the SNAIL level, RH30 cells were transduced with shRNA lentiviral vectors targeting SNAIL (shSNAIL) and control vectors (shCTRL), and these cells were selected with puromycin. SNAIL silencing was validated by qPCR ( n = 3) and Western blotting (total cell extracts). c Stable SNAIL silencing in RH30 cells leads to the acquisition of a spindle- shaped phenotype and reorganization of the cytoskeleton. The morphology of RH30 cells differentiated for 4 days was visualized with Wright’s staining and for 6 days with phase contrast microscopy. d SNAIL silencing and the differentiation of RH30 cells led to cell cycle arrest at the G0-G1 phase and diminished percentage of the cells in S phase. RH30 cells were differentiated for 7 days in medium containing 2% HS. Subsequently, the cell cycle and BrdU incorporation in S phase were analyzed by flow cytometry—the cells were stained with anti-BrdU antibody conjugated with APC and with 7AAD. The data in the graphs represent the mean ± SEM or are representative images of at least 3 independent experiments. * p

Techniques Used: Transfection, Sequencing, Real-time Polymerase Chain Reaction, Staining, MTS Assay, Stable Transfection, Transduction, shRNA, Western Blot, Microscopy, BrdU Incorporation Assay, Flow Cytometry, Cytometry

SNAIL silencing induces MYF5 expression in ARMS cells. a SNAIL silencing does not significantly affect MYOD expression at the mRNA (qPCR, n = 3) or protein level (Western blot) in undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium with 2% HS. b MYF5 is expressed in the nuclei of RH30 shSNAIL cells. The MYF5 protein level was visualized by Western blot and by immunofluorescent staining (red color), and the nuclei were visualized with DAPI (blue). The results are presented as merged images. The white scale bar represents 10 μm. c SNAIL silencing induces the expression of MYF5 mRNA in both undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium with 2% HS (qPCR, n = 3) d SNAIL silencing slightly induces the expression of MYF5 mRNA in both undifferentiated RH41 cells and RH41 cells differentiated for 7 days in medium with 2% HS (qPCR, n = 3). e Transient SNAIL silencing with siRNA in RH30 and RH41 ARMS cell lines slightly induces MYF5 expression. The cells were transfected with siRNA against SNAIL (siSNAIL) and a scrambled siRNA sequence (siRNA). Twenty-four hours after transfection, the cells were treated with differentiating medium containing 2% HS for the following 48 h. MYF5 levels were validated by qPCR; n = 3. f Transfection with pre-miR-30a-5p in RH30 cells induces MYF5 expression by downregulation of SNAIL protein. RH30 cells were transfected with the miRNA precursor pre-miR-30a-5p and pre-miR negative control (miR-neg-ctrl). Twenty-four hours after transfection, the cells were treated with differentiating medium containing 2% HS for the following 48 h. miR-30a-5p expression relative to U6 snRNA and MYF5, MYOD expression relative to GAPDH were validated by qPCR; n = 4. SNAIL protein level was validated by Western blot. The data represent the mean ± SEM. * p
Figure Legend Snippet: SNAIL silencing induces MYF5 expression in ARMS cells. a SNAIL silencing does not significantly affect MYOD expression at the mRNA (qPCR, n = 3) or protein level (Western blot) in undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium with 2% HS. b MYF5 is expressed in the nuclei of RH30 shSNAIL cells. The MYF5 protein level was visualized by Western blot and by immunofluorescent staining (red color), and the nuclei were visualized with DAPI (blue). The results are presented as merged images. The white scale bar represents 10 μm. c SNAIL silencing induces the expression of MYF5 mRNA in both undifferentiated RH30 cells and RH30 cells differentiated for 7 days in medium with 2% HS (qPCR, n = 3) d SNAIL silencing slightly induces the expression of MYF5 mRNA in both undifferentiated RH41 cells and RH41 cells differentiated for 7 days in medium with 2% HS (qPCR, n = 3). e Transient SNAIL silencing with siRNA in RH30 and RH41 ARMS cell lines slightly induces MYF5 expression. The cells were transfected with siRNA against SNAIL (siSNAIL) and a scrambled siRNA sequence (siRNA). Twenty-four hours after transfection, the cells were treated with differentiating medium containing 2% HS for the following 48 h. MYF5 levels were validated by qPCR; n = 3. f Transfection with pre-miR-30a-5p in RH30 cells induces MYF5 expression by downregulation of SNAIL protein. RH30 cells were transfected with the miRNA precursor pre-miR-30a-5p and pre-miR negative control (miR-neg-ctrl). Twenty-four hours after transfection, the cells were treated with differentiating medium containing 2% HS for the following 48 h. miR-30a-5p expression relative to U6 snRNA and MYF5, MYOD expression relative to GAPDH were validated by qPCR; n = 4. SNAIL protein level was validated by Western blot. The data represent the mean ± SEM. * p

Techniques Used: Expressing, Real-time Polymerase Chain Reaction, Western Blot, Staining, Transfection, Sequencing, Negative Control

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