Structured Review

TaKaRa scaffold 6
Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of <t>scaffold</t> 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
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Images

1) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

Techniques Used: Polymerase Chain Reaction, Sequencing

2) Product Images from "Involvement of MAFB and MAFF in Retinoid-Mediated Suppression of Hepatocellular Carcinoma Invasion"

Article Title: Involvement of MAFB and MAFF in Retinoid-Mediated Suppression of Hepatocellular Carcinoma Invasion

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms19051450

Gene expression in different types of liver diseases. Box and whisker plots of relative gene expression levels of TFPI2, RARα, RARβ, MAFB, and MAFF to β-actin in normal (N, n = 8; blue), fatty (FL, n = 5; green), hepatitis (Hs, n = 3; yellow), cirrhotic (Cir, n = 5; orange), and hepatocellular carcinoma (Tu, n = 23; red) liver tissues. Boxes indicate first and third quartiles and median values and whiskers represent 5 and 95 percentiles. Open circulars indicate outliers. * p
Figure Legend Snippet: Gene expression in different types of liver diseases. Box and whisker plots of relative gene expression levels of TFPI2, RARα, RARβ, MAFB, and MAFF to β-actin in normal (N, n = 8; blue), fatty (FL, n = 5; green), hepatitis (Hs, n = 3; yellow), cirrhotic (Cir, n = 5; orange), and hepatocellular carcinoma (Tu, n = 23; red) liver tissues. Boxes indicate first and third quartiles and median values and whiskers represent 5 and 95 percentiles. Open circulars indicate outliers. * p

Techniques Used: Expressing, Whisker Assay

ATRA-induced TFPI2 expression in HuH7 cells. ( A ) Dose-dependent expression of TFPI2 (red) and RARβ (blue) mRNA in HuH7 ( left ) and HepG2 ( right ) cells following incubation with ATRA for 12 h ( n = 4). * p
Figure Legend Snippet: ATRA-induced TFPI2 expression in HuH7 cells. ( A ) Dose-dependent expression of TFPI2 (red) and RARβ (blue) mRNA in HuH7 ( left ) and HepG2 ( right ) cells following incubation with ATRA for 12 h ( n = 4). * p

Techniques Used: Expressing, Incubation

Abrogation of the suppressive effect of ATRA on HuH7 cell invasion by TFPI2 knockdown. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shTFPI2-1, and shTFPI2-2 (NT, T2KD-1, and T2KD-2 cells, respectively). The cells were treated with EtOH (blue) and 2 µM ATRA (red) for 12 h ( n = 4). * p
Figure Legend Snippet: Abrogation of the suppressive effect of ATRA on HuH7 cell invasion by TFPI2 knockdown. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shTFPI2-1, and shTFPI2-2 (NT, T2KD-1, and T2KD-2 cells, respectively). The cells were treated with EtOH (blue) and 2 µM ATRA (red) for 12 h ( n = 4). * p

Techniques Used: Expressing, Stable Transfection, Transfection

Kaplan–Meier analyses of disease-free survival of HCC patients from the TCGA cohort. ( A , B ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFB expression in HCC with higher TFPI2 ( n = 68 or n = 93, respectively) ( A ) or higher MAFF ( n = 83 or 70, respectively) ( B ) groups, ( C , D ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFF expression in HCC with lower TFPI2 ( n = 94 or n = 62, respectively) ( C ) or lower MAFB ( n = 73 or n = 83, respectively) ( D ) groups. P values shown were calculated by log-rank test. Median values of gene expression were used to divide the patients into the higher or lower groups.
Figure Legend Snippet: Kaplan–Meier analyses of disease-free survival of HCC patients from the TCGA cohort. ( A , B ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFB expression in HCC with higher TFPI2 ( n = 68 or n = 93, respectively) ( A ) or higher MAFF ( n = 83 or 70, respectively) ( B ) groups, ( C , D ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFF expression in HCC with lower TFPI2 ( n = 94 or n = 62, respectively) ( C ) or lower MAFB ( n = 73 or n = 83, respectively) ( D ) groups. P values shown were calculated by log-rank test. Median values of gene expression were used to divide the patients into the higher or lower groups.

Techniques Used: Expressing

Transcriptional regulation of TFPI2 expression by ATRA in HuH7 cells. ( A , B ) HuH7 ( A ) and HepG2 ( B ) cells pre-treated with ActD incubated with EtOH (blue) and 2 µM ATRA (red) for the indicated times. Left, RARβ, right, TFPI2 ( n = 4); ( C ) HuH7 and HepG2 cells pre-treated with N -hydroxy- N ′-phenyloctanediamide (SAHA) (blue) and AzC (red) incubated with EtOH and 2 µM ATRA for 12 h. RARβ ( Left ), TFPI2 ( right ) ( n = 4). * p
Figure Legend Snippet: Transcriptional regulation of TFPI2 expression by ATRA in HuH7 cells. ( A , B ) HuH7 ( A ) and HepG2 ( B ) cells pre-treated with ActD incubated with EtOH (blue) and 2 µM ATRA (red) for the indicated times. Left, RARβ, right, TFPI2 ( n = 4); ( C ) HuH7 and HepG2 cells pre-treated with N -hydroxy- N ′-phenyloctanediamide (SAHA) (blue) and AzC (red) incubated with EtOH and 2 µM ATRA for 12 h. RARβ ( Left ), TFPI2 ( right ) ( n = 4). * p

Techniques Used: Expressing, Incubation

Regulation of human TFPI2 promoter by RARα, MAFB, and MAFF. ( A , B ) A luciferase reporter vector driven by the human TFPI2 promoter was transfected along with pDNA expressing the indicated transcription factor genes with ( B ) and without ( A ) RARα-pDNA into HuH7 cells ( n = 4). Twenty-four hours after transfection, EtOH (blue) and 2 µM ATRA (red) were added to the cells, and further incubated for 24 h, which was followed by dual luciferase assay. * p
Figure Legend Snippet: Regulation of human TFPI2 promoter by RARα, MAFB, and MAFF. ( A , B ) A luciferase reporter vector driven by the human TFPI2 promoter was transfected along with pDNA expressing the indicated transcription factor genes with ( B ) and without ( A ) RARα-pDNA into HuH7 cells ( n = 4). Twenty-four hours after transfection, EtOH (blue) and 2 µM ATRA (red) were added to the cells, and further incubated for 24 h, which was followed by dual luciferase assay. * p

Techniques Used: Luciferase, Plasmid Preparation, Transfection, Expressing, Incubation

Effect of RARα, MAFB, and MAFF on HuH7 cell invasion through TFPI2. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shRARα, shMAFB, or shMAFF (NT, RaKD, MBKD, and MFKD cells, respectively). The cells were treated with EtOH (blue) or 2 µM ATRA (red) for 12 h ( n = 4). * p
Figure Legend Snippet: Effect of RARα, MAFB, and MAFF on HuH7 cell invasion through TFPI2. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shRARα, shMAFB, or shMAFF (NT, RaKD, MBKD, and MFKD cells, respectively). The cells were treated with EtOH (blue) or 2 µM ATRA (red) for 12 h ( n = 4). * p

Techniques Used: Expressing, Stable Transfection, Transfection

3) Product Images from "Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis"

Article Title: Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis

Journal: Scientific Reports

doi: 10.1038/s41598-017-14418-5

Variant structures of the novel TACC2 isoforms. Three known isoforms and the novel isoforms of TACC2 are shown. Exons are depicted as boxes with introns as intervening lines; coding sequences (CDSs) and untranslated regions (UTRs) are depicted as black and gray, respectively. Structural features of TACC2 protein, such as TACC2 domain, are indicated in red. Variable regions are indicated in light blue. Insertions are indicated with white font with blue background, and deletions are indicated by a dotted line.
Figure Legend Snippet: Variant structures of the novel TACC2 isoforms. Three known isoforms and the novel isoforms of TACC2 are shown. Exons are depicted as boxes with introns as intervening lines; coding sequences (CDSs) and untranslated regions (UTRs) are depicted as black and gray, respectively. Structural features of TACC2 protein, such as TACC2 domain, are indicated in red. Variable regions are indicated in light blue. Insertions are indicated with white font with blue background, and deletions are indicated by a dotted line.

Techniques Used: Variant Assay

4) Product Images from "One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)"

Article Title: One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)

Journal: BMC Genomics

doi: 10.1186/s12864-015-1432-5

Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .
Figure Legend Snippet: Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .

Techniques Used: Injection, Polymerase Chain Reaction, Nested PCR, Derivative Assay, Fluorescence

5) Product Images from "Loss of MYC and E-box3 binding contributes to defective MYC-mediated transcriptional suppression of human MC-let-7a-1~let-7d in glioblastoma"

Article Title: Loss of MYC and E-box3 binding contributes to defective MYC-mediated transcriptional suppression of human MC-let-7a-1~let-7d in glioblastoma

Journal: Oncotarget

doi: 10.18632/oncotarget.10517

MC-let-7a-1~let-7d promoter characterization in GBM as compared to that in HCC ( A ) primers used for 5′RACE. Gene-specific primers (GSPs) GSP1-1 was used to synthesize the first strand cDNA. Primary amplification was carried out with abridged anchor primer (AAP) and GSP2-1 primer. Nested PCR was performed with abridged universal amplification primer (AUAP) and GSP2-2.( B ) 5′RACE results. The ~700-bp products were amplified in U87 cells and U251 cells by using GSP2-2 and AUAP. ( C ) sequence analysis of 20 products from each cell lines revealed that variable TSSs were used. The major TSSs of MC-let-7a-1~let-7d in U87 is located about 28 bp, while in U251 is located about 40 bp downstream of the TSSs used in HepG2 cells. ( D ) schematic diagram of the reporter construct (left panel). Truncation of the downstream region to +1 dramatically improved the promoter activity, whereas truncation of the upstream region to −227 resulted in progressive loss of activity in both U87 cells and L02 cells.
Figure Legend Snippet: MC-let-7a-1~let-7d promoter characterization in GBM as compared to that in HCC ( A ) primers used for 5′RACE. Gene-specific primers (GSPs) GSP1-1 was used to synthesize the first strand cDNA. Primary amplification was carried out with abridged anchor primer (AAP) and GSP2-1 primer. Nested PCR was performed with abridged universal amplification primer (AUAP) and GSP2-2.( B ) 5′RACE results. The ~700-bp products were amplified in U87 cells and U251 cells by using GSP2-2 and AUAP. ( C ) sequence analysis of 20 products from each cell lines revealed that variable TSSs were used. The major TSSs of MC-let-7a-1~let-7d in U87 is located about 28 bp, while in U251 is located about 40 bp downstream of the TSSs used in HepG2 cells. ( D ) schematic diagram of the reporter construct (left panel). Truncation of the downstream region to +1 dramatically improved the promoter activity, whereas truncation of the upstream region to −227 resulted in progressive loss of activity in both U87 cells and L02 cells.

Techniques Used: Amplification, Nested PCR, Sequencing, Construct, Activity Assay

6) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.
Figure Legend Snippet: Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.

Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Negative Control

7) Product Images from "Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain"

Article Title: Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.03603-15

Curing pTT27 from T. thermophilus HB27. (A) Strategy to cure the pTT27 megaplasmid from HB27. When HB27 was transformed by pUC27H11, the intact pTT27 was excluded due to plasmid incompatibility. The transformant lacking pTT27 but containing pUC27H11 was
Figure Legend Snippet: Curing pTT27 from T. thermophilus HB27. (A) Strategy to cure the pTT27 megaplasmid from HB27. When HB27 was transformed by pUC27H11, the intact pTT27 was excluded due to plasmid incompatibility. The transformant lacking pTT27 but containing pUC27H11 was

Techniques Used: Transformation Assay, Plasmid Preparation

8) Product Images from "Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk"

Article Title: Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.69.12.7224-7235.2003

Summary pie charts of archaeal and bacterial phylotype compositions for 16S rRNA gene clone libraries constructed from pelagic clay and volcanic ash layers in the MD01-2412 Okhotsk core sediments. MHVG, marine hydrothermal vent group; MG1, marine group 1; MBG-D, marine benthic group D; SAGMEG, South American gold mine euryarchaeotic group; α, alpha subclass of the class Proteobacteria ; γ, gamma subclass of the class Proteobacteria ; δ, delta subclass of the class Proteobacteria .
Figure Legend Snippet: Summary pie charts of archaeal and bacterial phylotype compositions for 16S rRNA gene clone libraries constructed from pelagic clay and volcanic ash layers in the MD01-2412 Okhotsk core sediments. MHVG, marine hydrothermal vent group; MG1, marine group 1; MBG-D, marine benthic group D; SAGMEG, South American gold mine euryarchaeotic group; α, alpha subclass of the class Proteobacteria ; γ, gamma subclass of the class Proteobacteria ; δ, delta subclass of the class Proteobacteria .

Techniques Used: Construct

Profiles of archaeal and bacterial communities in 16S rRNA gene clone libraries constructed for various depths of pelagic clay and volcanic ash layers. The numbers of clones examined are indicated in parentheses. The percentages of the cloned sequences affiliated with the phylogenetic groups are indicated by the bar graphs. Sec., section; mbsf, meters below the seafloor.
Figure Legend Snippet: Profiles of archaeal and bacterial communities in 16S rRNA gene clone libraries constructed for various depths of pelagic clay and volcanic ash layers. The numbers of clones examined are indicated in parentheses. The percentages of the cloned sequences affiliated with the phylogenetic groups are indicated by the bar graphs. Sec., section; mbsf, meters below the seafloor.

Techniques Used: Construct, Clone Assay, Size-exclusion Chromatography

Profiles of total cell density (A) and 16S rRNA gene concentration (B) in the MD01-2412 core sediments. (A) Total cell densities in pelagic clay samples (○) and ash layer samples (•) were estimated by direct counting of AO-stained cells. (B) Archaeal (□) and bacterial (▪) concentrations of the 16S rRNA gene were determined by quantitative PCR by using domain-specific fluorogenic probes. mbsf, meters below the seafloor; rDNA, ribosomal DNA.
Figure Legend Snippet: Profiles of total cell density (A) and 16S rRNA gene concentration (B) in the MD01-2412 core sediments. (A) Total cell densities in pelagic clay samples (○) and ash layer samples (•) were estimated by direct counting of AO-stained cells. (B) Archaeal (□) and bacterial (▪) concentrations of the 16S rRNA gene were determined by quantitative PCR by using domain-specific fluorogenic probes. mbsf, meters below the seafloor; rDNA, ribosomal DNA.

Techniques Used: Concentration Assay, Staining, Real-time Polymerase Chain Reaction

Phylogenetic relationships of archaeal 16S rRNA gene sequences of representative clones from the Okhotsk core sediments and of related pure cultures and environmental clones in the kingdoms Crenarchaeota (A) and Euryarchaeota (B). The trees were inferred by neighbor-joining analysis by using restricted homologous positions of 16S rRNA gene sequences. The solid circles at nodes indicate positions where the confidence value for 100 bootstrap trial results is less than 40%. The sequences of representative clones determined in this study are indicated by boldface type. The numbers in parentheses are accession numbers of sequences. Scale bar = 0.02 nucleotide substitution per sequence position.
Figure Legend Snippet: Phylogenetic relationships of archaeal 16S rRNA gene sequences of representative clones from the Okhotsk core sediments and of related pure cultures and environmental clones in the kingdoms Crenarchaeota (A) and Euryarchaeota (B). The trees were inferred by neighbor-joining analysis by using restricted homologous positions of 16S rRNA gene sequences. The solid circles at nodes indicate positions where the confidence value for 100 bootstrap trial results is less than 40%. The sequences of representative clones determined in this study are indicated by boldface type. The numbers in parentheses are accession numbers of sequences. Scale bar = 0.02 nucleotide substitution per sequence position.

Techniques Used: Clone Assay, Sequencing

Phylogenetic relationships of bacterial 16S rRNA gene sequences of representative clones from the Okhotsk core sediments and related pure cultures and environmental clones belonging to the class Proteobacteria (A) and to the Dehalococcoides ). The trees were inferred by neighbor-joining analysis by using restricted homologous positions of 16S rRNA gene sequences. The solid circles at nodes indicate positions where the confidence value for 100 bootstrap trial results is less than 40%. 16S rRNA gene sequences of representative clones and isolates determined in this study are indicated by boldface type. The numbers in parentheses are accession numbers of sequences. Scale bar = 0.02 nucleotide substitution per sequence position.
Figure Legend Snippet: Phylogenetic relationships of bacterial 16S rRNA gene sequences of representative clones from the Okhotsk core sediments and related pure cultures and environmental clones belonging to the class Proteobacteria (A) and to the Dehalococcoides ). The trees were inferred by neighbor-joining analysis by using restricted homologous positions of 16S rRNA gene sequences. The solid circles at nodes indicate positions where the confidence value for 100 bootstrap trial results is less than 40%. 16S rRNA gene sequences of representative clones and isolates determined in this study are indicated by boldface type. The numbers in parentheses are accession numbers of sequences. Scale bar = 0.02 nucleotide substitution per sequence position.

Techniques Used: Clone Assay, Sequencing

9) Product Images from "Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis"

Article Title: Promoter-level transcriptome in primary lesions of endometrial cancer identified biomarkers associated with lymph node metastasis

Journal: Scientific Reports

doi: 10.1038/s41598-017-14418-5

Variant structures of the novel TACC2 isoforms. Three known isoforms and the novel isoforms of TACC2 are shown. Exons are depicted as boxes with introns as intervening lines; coding sequences (CDSs) and untranslated regions (UTRs) are depicted as black and gray, respectively. Structural features of TACC2 protein, such as TACC2 domain, are indicated in red. Variable regions are indicated in light blue. Insertions are indicated with white font with blue background, and deletions are indicated by a dotted line.
Figure Legend Snippet: Variant structures of the novel TACC2 isoforms. Three known isoforms and the novel isoforms of TACC2 are shown. Exons are depicted as boxes with introns as intervening lines; coding sequences (CDSs) and untranslated regions (UTRs) are depicted as black and gray, respectively. Structural features of TACC2 protein, such as TACC2 domain, are indicated in red. Variable regions are indicated in light blue. Insertions are indicated with white font with blue background, and deletions are indicated by a dotted line.

Techniques Used: Variant Assay

10) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

Techniques Used: Polymerase Chain Reaction, Sequencing

Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.
Figure Legend Snippet: Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.

Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Negative Control

11) Product Images from "Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR"

Article Title: Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR

Journal: Journal of Nucleic Acids

doi: 10.1155/2013/823730

The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.
Figure Legend Snippet: The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.

Techniques Used: Polymerase Chain Reaction, Generated, Amplification, Software

Various target sequences were amplified in the presence of ttRecA and ttMutS. (a) A 611 bp region of the ttha0122 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. The amounts of amplified fragments were quantified and are shown as bar graphs in the lower panel. Gray and blue bars indicate nonspecific and desired amplifications, respectively. (b) A 423 bp region of the ttha1806 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. (c) A 466 bp region of the ttha1300 gene was amplified from T. thermophilus HB8 genomic DNA in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttMutS were used here. (d) A 1,278 bp region of the ttha1548 gene was amplified in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttRecA were used here.
Figure Legend Snippet: Various target sequences were amplified in the presence of ttRecA and ttMutS. (a) A 611 bp region of the ttha0122 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. The amounts of amplified fragments were quantified and are shown as bar graphs in the lower panel. Gray and blue bars indicate nonspecific and desired amplifications, respectively. (b) A 423 bp region of the ttha1806 gene was amplified from T. thermophilus HB8 genomic DNA template in the presence of ttRecA and ttMutS. (c) A 466 bp region of the ttha1300 gene was amplified from T. thermophilus HB8 genomic DNA in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttMutS were used here. (d) A 1,278 bp region of the ttha1548 gene was amplified in the presence of ttRecA or ttMutS. Note that relatively high concentrations of ttRecA were used here.

Techniques Used: Amplification

12) Product Images from "Identification of the Minus-Dominance Gene Ortholog in the Mating-Type Locus of Gonium pectorale"

Article Title: Identification of the Minus-Dominance Gene Ortholog in the Mating-Type Locus of Gonium pectorale

Journal: Genetics

doi: 10.1534/genetics.107.078618

Scoring the nuclear markers in the F 1 progeny. A sampling of the DNA gel blot and PCR–RFLP analyses on G. pectorale progeny strains for the six nuclear markers. Diploid strains are marked with asterisks. Parental strains were Mongolia 1 (M1) and
Figure Legend Snippet: Scoring the nuclear markers in the F 1 progeny. A sampling of the DNA gel blot and PCR–RFLP analyses on G. pectorale progeny strains for the six nuclear markers. Diploid strains are marked with asterisks. Parental strains were Mongolia 1 (M1) and

Techniques Used: Sampling, Western Blot, Polymerase Chain Reaction

13) Product Images from "Potential Spermatogenesis Recovery with Bone Marrow Mesenchymal Stem Cells in an Azoospermic Rat Model"

Article Title: Potential Spermatogenesis Recovery with Bone Marrow Mesenchymal Stem Cells in an Azoospermic Rat Model

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms150813151

Relative level of spermatogenic specific genes expression in recipient rat testicular tissue after BMSCs transplantation detected by real time PCR. Vasa, dazl, smad1 and stella expression were detected 2 weeks post-transplantation and increased to a relatively high level at 4 to 8 weeks. C-kit and GCNF were expressed at relatively high levels immediately after injection, and expression levels decreased to almost zero within 2 weeks. GCNF expression increased gradually at 4 weeks post-transplantation, while expression of c-kit remained at a relatively low level.
Figure Legend Snippet: Relative level of spermatogenic specific genes expression in recipient rat testicular tissue after BMSCs transplantation detected by real time PCR. Vasa, dazl, smad1 and stella expression were detected 2 weeks post-transplantation and increased to a relatively high level at 4 to 8 weeks. C-kit and GCNF were expressed at relatively high levels immediately after injection, and expression levels decreased to almost zero within 2 weeks. GCNF expression increased gradually at 4 weeks post-transplantation, while expression of c-kit remained at a relatively low level.

Techniques Used: Expressing, Transplantation Assay, Real-time Polymerase Chain Reaction, Injection

14) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

Techniques Used: Polymerase Chain Reaction, Sequencing

Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.
Figure Legend Snippet: Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.

Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Negative Control

15) Product Images from "Reactivation of FMR1 by CRISPR/Cas9-Mediated Deletion of the Expanded CGG-Repeat of the Fragile X Chromosome"

Article Title: Reactivation of FMR1 by CRISPR/Cas9-Mediated Deletion of the Expanded CGG-Repeat of the Fragile X Chromosome

Journal: PLoS ONE

doi: 10.1371/journal.pone.0165499

Methylation profiling analysis of CRISPR cut clonal lines derived from somatic hybrid CHO cells and iPS cells. DNA methylation profiling analysis was performed using Infinium HumanMethylation450 BeadChip. Data analysis was focused on the 8 probe positions at the promoter region of FMR1 gene. Silent clonal lines were shown in red, and expressing clonal lines were shown in blue. (A) Methylation states of CRISPR cut somatic hybrid CHO cells. (B) Methylation states of CRISPR cut iPS cells.
Figure Legend Snippet: Methylation profiling analysis of CRISPR cut clonal lines derived from somatic hybrid CHO cells and iPS cells. DNA methylation profiling analysis was performed using Infinium HumanMethylation450 BeadChip. Data analysis was focused on the 8 probe positions at the promoter region of FMR1 gene. Silent clonal lines were shown in red, and expressing clonal lines were shown in blue. (A) Methylation states of CRISPR cut somatic hybrid CHO cells. (B) Methylation states of CRISPR cut iPS cells.

Techniques Used: Methylation, CRISPR, Derivative Assay, DNA Methylation Assay, Expressing

16) Product Images from "Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways"

Article Title: Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways

Journal: Antonie Van Leeuwenhoek

doi: 10.1007/s10482-009-9400-1

Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5
Figure Legend Snippet: Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5

Techniques Used: Agarose Gel Electrophoresis, Marker

17) Product Images from "The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide-disulfide reductase family"

Article Title: The orphan protein bis-γ-glutamylcystine reductase joins the pyridine nucleotide-disulfide reductase family

Journal: Biochemistry

doi: 10.1021/bi4003343

(A) SDS-PAGE analysis of Halobacterium sp. NRC-1 N-His 6 -GCR overproduced in E. coli Arctic (DE3) RP. Lane 1, lysate; lane 2, soluble supernatant; lane 3, insoluble precipitate; lane 4, refolded protein; lane 5, protein obtained after purification using an immobilized Cu 2+ resin. (B) GCR activity of the purified protein as a function of bis-γ-glutamylcystine concentration.
Figure Legend Snippet: (A) SDS-PAGE analysis of Halobacterium sp. NRC-1 N-His 6 -GCR overproduced in E. coli Arctic (DE3) RP. Lane 1, lysate; lane 2, soluble supernatant; lane 3, insoluble precipitate; lane 4, refolded protein; lane 5, protein obtained after purification using an immobilized Cu 2+ resin. (B) GCR activity of the purified protein as a function of bis-γ-glutamylcystine concentration.

Techniques Used: SDS Page, Purification, Activity Assay, Concentration Assay

18) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

Techniques Used: Polymerase Chain Reaction, Sequencing

Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.
Figure Legend Snippet: Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.

Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Negative Control

19) Product Images from "Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways"

Article Title: Genetic and phenotypic diversity of Ralstonia solanacearum biovar 2 strains obtained from Dutch waterways

Journal: Antonie Van Leeuwenhoek

doi: 10.1007/s10482-009-9400-1

Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5
Figure Legend Snippet: Agarose gel showing fingerprints of the hrp region (primer set pglA-F2 and hrcV-R2) after restriction with ( a ) HinfI and ( b ) RsaI . Lane M is Kb+ molecular size marker, lane 1 is strain 1609; lane 2 is strain KZR-5

Techniques Used: Agarose Gel Electrophoresis, Marker

20) Product Images from "Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk"

Article Title: Microbial Communities Associated with Geological Horizons in Coastal Subseafloor Sediments from the Sea of Okhotsk

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.69.12.7224-7235.2003

Profiles of total cell density (A) and 16S rRNA gene concentration (B) in the MD01-2412 core sediments. (A) Total cell densities in pelagic clay samples (○) and ash layer samples (•) were estimated by direct counting of AO-stained cells. (B) Archaeal (□) and bacterial (▪) concentrations of the 16S rRNA gene were determined by quantitative PCR by using domain-specific fluorogenic probes. mbsf, meters below the seafloor; rDNA, ribosomal DNA.
Figure Legend Snippet: Profiles of total cell density (A) and 16S rRNA gene concentration (B) in the MD01-2412 core sediments. (A) Total cell densities in pelagic clay samples (○) and ash layer samples (•) were estimated by direct counting of AO-stained cells. (B) Archaeal (□) and bacterial (▪) concentrations of the 16S rRNA gene were determined by quantitative PCR by using domain-specific fluorogenic probes. mbsf, meters below the seafloor; rDNA, ribosomal DNA.

Techniques Used: Concentration Assay, Staining, Real-time Polymerase Chain Reaction

21) Product Images from "Activation of TonEBP by Calcium Controls β1,3-Glucuronosyltransferase-I Expression, a Key Regulator of Glycosaminoglycan Synthesis in Cells of the Intervertebral Disc"

Article Title: Activation of TonEBP by Calcium Controls β1,3-Glucuronosyltransferase-I Expression, a Key Regulator of Glycosaminoglycan Synthesis in Cells of the Intervertebral Disc

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M807081200

GlcAT-I promoter activity suppressed by NFAT signaling in nucleus pulposus cells. Effect of NFAT vectors (NFAT1, -2, -3, and -4) and/or CnA and CnB on GlcAT-I-D reporter activity of nucleus pulposus cells. A , NFAT1 alone did not affect GlcAT-I reporter activity. When calcineurin was added alone or together with NFAT1, there was a suppression in reporter activity. CA-NFAT2 ( B ), NFAT3 ( C ), or NFAT4 ( D ) alone or when added with CnA/B significantly suppressed the GlcAT-I-D reporter activity in nucleus pulposus cells. E , nucleus pulposus cells were transfected with 3×NFAT luciferase construct with or without NFAT1, CA-NFAT2, NFAT3, or NFAT4, and reporter activity was measured. Co-expression of NFAT1 to -4 resulted in a significant increase in activity of 3×NFAT reporter plasmid, indicating functionality of expressed proteins. Values shown are mean ± S.D., of three independent experiments. *, p
Figure Legend Snippet: GlcAT-I promoter activity suppressed by NFAT signaling in nucleus pulposus cells. Effect of NFAT vectors (NFAT1, -2, -3, and -4) and/or CnA and CnB on GlcAT-I-D reporter activity of nucleus pulposus cells. A , NFAT1 alone did not affect GlcAT-I reporter activity. When calcineurin was added alone or together with NFAT1, there was a suppression in reporter activity. CA-NFAT2 ( B ), NFAT3 ( C ), or NFAT4 ( D ) alone or when added with CnA/B significantly suppressed the GlcAT-I-D reporter activity in nucleus pulposus cells. E , nucleus pulposus cells were transfected with 3×NFAT luciferase construct with or without NFAT1, CA-NFAT2, NFAT3, or NFAT4, and reporter activity was measured. Co-expression of NFAT1 to -4 resulted in a significant increase in activity of 3×NFAT reporter plasmid, indicating functionality of expressed proteins. Values shown are mean ± S.D., of three independent experiments. *, p

Techniques Used: Activity Assay, Transfection, Luciferase, Construct, Expressing, Plasmid Preparation

GlcAT-I promoter contains TonEBP and NFAT binding motifs. A , promoter organization of the human GlcAT-I gene. The transcription start site is marked as + 1 . The TonE site is shown as a flattened circle , Spls are indicted as ovals , and the NFAT binding motifs are shown as rectangles . B , DNA sequence of the promoter region of the human GlcAT-I gene. TonE (TTTCCA) and NFAT (TTTCC or GGAAA) consensus sequences are marked in boldface type and underlined . The arrows indicate the starting location of the primers used to generate promoter constructs. The transcription start site is marked as + 1 ; ATG marks the translation start site. Spl sites are underlined and lie within first 100 bases. C , schematic diagram showing a map of successive PCR-generated 5′ deletion constructs of the human GlcAT-I promoter. The GlcAT-I-D construct consists of a 1,231-bp fragment containing 1,170 bp of the upstream GlcAT-I promoter sequence linked to 61 bp of exon 1 ( i.e. –1170/+61), whereas GlcAT-I-M and GlcAT-I-P constructs contain a 335-bp fragment (–274/+61) and a 184-bp fragment (–123/+61), respectively. D , basal activities of GlcAT-I promoter constructs relative to full-length construct GlcAT-I-D in nucleus pulposus cells. Cells showed maximal luciferase activity for the GlcAT-I-D construct, whereas the shortest construct, GlcAT-I-P, showed minimal activity. Values shown are mean ± S.D. of three independent experiments. *, p
Figure Legend Snippet: GlcAT-I promoter contains TonEBP and NFAT binding motifs. A , promoter organization of the human GlcAT-I gene. The transcription start site is marked as + 1 . The TonE site is shown as a flattened circle , Spls are indicted as ovals , and the NFAT binding motifs are shown as rectangles . B , DNA sequence of the promoter region of the human GlcAT-I gene. TonE (TTTCCA) and NFAT (TTTCC or GGAAA) consensus sequences are marked in boldface type and underlined . The arrows indicate the starting location of the primers used to generate promoter constructs. The transcription start site is marked as + 1 ; ATG marks the translation start site. Spl sites are underlined and lie within first 100 bases. C , schematic diagram showing a map of successive PCR-generated 5′ deletion constructs of the human GlcAT-I promoter. The GlcAT-I-D construct consists of a 1,231-bp fragment containing 1,170 bp of the upstream GlcAT-I promoter sequence linked to 61 bp of exon 1 ( i.e. –1170/+61), whereas GlcAT-I-M and GlcAT-I-P constructs contain a 335-bp fragment (–274/+61) and a 184-bp fragment (–123/+61), respectively. D , basal activities of GlcAT-I promoter constructs relative to full-length construct GlcAT-I-D in nucleus pulposus cells. Cells showed maximal luciferase activity for the GlcAT-I-D construct, whereas the shortest construct, GlcAT-I-P, showed minimal activity. Values shown are mean ± S.D. of three independent experiments. *, p

Techniques Used: Binding Assay, Sequencing, Construct, Polymerase Chain Reaction, Generated, Luciferase, Activity Assay

Calcineurin suppresses GlcAT-I promoter function. A , the GlcAT-I reporter activity following cotransfection with calcineurin A/B constructs or empty vector pBJ5 in nucleus pulposus cells. Co-expression of calcineurin subunits suppressed GlcAT-I reporter activity in transfected cells. B–F , reporter activity of medullary fibroblasts derived from CnA WT or CnAα or CnAβ null (–/–) mice transfected with GlcAT-I or tauT (WT or MT) reporter and treated with ionomycin and PMA with or without FK506 and CsA. Ionomycin did not increase GlcAT-I reporter activity in wild type cells ( B ), but a robust induction was observed in both the CnAα or CnAβ null cells ( C ). A similar high induction in the activity of tauT -WT reporter was observed in CnAα or CnAβ null cells; a relatively small inductive effect was seen in wild type cells, which remained constant after the addition of calcineurin inhibitors FK506 and CsA. Neither wild type ( D ) nor the null cells ( E and F ) displayed induction in tauT -MT reporter activity. Values shown are mean ± S.D. of three independent experiments performed in triplicate. *, p
Figure Legend Snippet: Calcineurin suppresses GlcAT-I promoter function. A , the GlcAT-I reporter activity following cotransfection with calcineurin A/B constructs or empty vector pBJ5 in nucleus pulposus cells. Co-expression of calcineurin subunits suppressed GlcAT-I reporter activity in transfected cells. B–F , reporter activity of medullary fibroblasts derived from CnA WT or CnAα or CnAβ null (–/–) mice transfected with GlcAT-I or tauT (WT or MT) reporter and treated with ionomycin and PMA with or without FK506 and CsA. Ionomycin did not increase GlcAT-I reporter activity in wild type cells ( B ), but a robust induction was observed in both the CnAα or CnAβ null cells ( C ). A similar high induction in the activity of tauT -WT reporter was observed in CnAα or CnAβ null cells; a relatively small inductive effect was seen in wild type cells, which remained constant after the addition of calcineurin inhibitors FK506 and CsA. Neither wild type ( D ) nor the null cells ( E and F ) displayed induction in tauT -MT reporter activity. Values shown are mean ± S.D. of three independent experiments performed in triplicate. *, p

Techniques Used: Activity Assay, Cotransfection, Construct, Plasmid Preparation, Expressing, Transfection, Derivative Assay, Mouse Assay

Ionomycin mediated induction of GlcAT-I promoter activity requires TonEBP binding to TonE. Effect of a 4-bp mutation introduced into the TonE motif of the GlcAT-I-D reporter plasmid. Nucleus pulposus cells were transfected with wild type GlcAT-I-D ( W-GlcAT-I ) or mutant GlcAT-I-D ( M-GlcAT-I ) reporter plasmids, and the induction of the luciferase activity was determined following ionomycin treatment. Treatment caused an induction of wild type reporter activity, whereas the mutant reporter failed to increase activity. Values shown are mean ± S.D. of three independent experiments. *, p
Figure Legend Snippet: Ionomycin mediated induction of GlcAT-I promoter activity requires TonEBP binding to TonE. Effect of a 4-bp mutation introduced into the TonE motif of the GlcAT-I-D reporter plasmid. Nucleus pulposus cells were transfected with wild type GlcAT-I-D ( W-GlcAT-I ) or mutant GlcAT-I-D ( M-GlcAT-I ) reporter plasmids, and the induction of the luciferase activity was determined following ionomycin treatment. Treatment caused an induction of wild type reporter activity, whereas the mutant reporter failed to increase activity. Values shown are mean ± S.D. of three independent experiments. *, p

Techniques Used: Activity Assay, Binding Assay, Mutagenesis, Plasmid Preparation, Transfection, Luciferase

Ionomycin mediates GlcAT-I promoter activation, although TonEBP is independent of calcineurin. Nucleus pulposus cells ( A ), TonEBP/NFAT5 wild type ( B ), and TonEBP/NFAT5 null ( C ) MEFs were transfected with GlcAT-I-D reporter, and activity was measured following treatment with ionomycin with or without FK506 and cyclosporine A. Unlike TonEBP/NFAT5, null MEFs GlcAT-I-D reporter activity was induced in both nucleus pulposus and NFAT5 wild type cells. Calcineurin inhibitors did not suppress ionomycin-induced or basal activity of GlcAT-I reporter in any of the cell types. D , effect of ionomycin treatment on GlcAT-I-P reporter activity. The reporter was nonresponsive to ionomycin treatment in both TonEBP/NFAT5 wild type and null MEFs. Values shown are mean ± S.D. of three independent experiments performed in triplicate. *, p
Figure Legend Snippet: Ionomycin mediates GlcAT-I promoter activation, although TonEBP is independent of calcineurin. Nucleus pulposus cells ( A ), TonEBP/NFAT5 wild type ( B ), and TonEBP/NFAT5 null ( C ) MEFs were transfected with GlcAT-I-D reporter, and activity was measured following treatment with ionomycin with or without FK506 and cyclosporine A. Unlike TonEBP/NFAT5, null MEFs GlcAT-I-D reporter activity was induced in both nucleus pulposus and NFAT5 wild type cells. Calcineurin inhibitors did not suppress ionomycin-induced or basal activity of GlcAT-I reporter in any of the cell types. D , effect of ionomycin treatment on GlcAT-I-P reporter activity. The reporter was nonresponsive to ionomycin treatment in both TonEBP/NFAT5 wild type and null MEFs. Values shown are mean ± S.D. of three independent experiments performed in triplicate. *, p

Techniques Used: Activation Assay, Transfection, Activity Assay

22) Product Images from "Establishment of nDart1-tagged lines of Koshihikari, an elite variety of rice in Japan"

Article Title: Establishment of nDart1-tagged lines of Koshihikari, an elite variety of rice in Japan

Journal: Breeding Science

doi: 10.1270/jsbbs.19049

Confirmation of nDart1-0 insertion revealed by TAIL-PCR. (A) GS (Green sector) and WS (White sector) in albino of Fig. 2B . (B) Banding pattern of WT, GS and WS using specific primers for each clone. White arrow and arrowhead indicate amplicons with nDart1 insertion and without nDart1 , respectively.
Figure Legend Snippet: Confirmation of nDart1-0 insertion revealed by TAIL-PCR. (A) GS (Green sector) and WS (White sector) in albino of Fig. 2B . (B) Banding pattern of WT, GS and WS using specific primers for each clone. White arrow and arrowhead indicate amplicons with nDart1 insertion and without nDart1 , respectively.

Techniques Used: Polymerase Chain Reaction

23) Product Images from "Exome sequencing reveals a novel MFN2 missense mutation in a Chinese family with Charcot-Marie-Tooth type 2A"

Article Title: Exome sequencing reveals a novel MFN2 missense mutation in a Chinese family with Charcot-Marie-Tooth type 2A

Journal: Experimental and Therapeutic Medicine

doi: 10.3892/etm.2018.6513

Identification of a missense mutation in the MFN2 gene. (A) The novel mutation c.1190G > C; p.(R397P) was verified by Sanger sequencing. (B) PCR-restriction fragment length polymorphism suggested the phenotype and genotype co-segregation in this pedigree. The nested PCR products of the affected family members (II3, II6, III2, III3, III4, III5 and IV1) were digested into two fragments (107 and 86 bp) by MSPI and the others were not affected. (C) Multi-species sequence alignment showing the evolutionarily conserved p.R397 position in MFN2. MFN2, mitofusin 2; PCR, polymerase chain reaction; M, molecular weight standards (50 bp DNA Ladder).
Figure Legend Snippet: Identification of a missense mutation in the MFN2 gene. (A) The novel mutation c.1190G > C; p.(R397P) was verified by Sanger sequencing. (B) PCR-restriction fragment length polymorphism suggested the phenotype and genotype co-segregation in this pedigree. The nested PCR products of the affected family members (II3, II6, III2, III3, III4, III5 and IV1) were digested into two fragments (107 and 86 bp) by MSPI and the others were not affected. (C) Multi-species sequence alignment showing the evolutionarily conserved p.R397 position in MFN2. MFN2, mitofusin 2; PCR, polymerase chain reaction; M, molecular weight standards (50 bp DNA Ladder).

Techniques Used: Mutagenesis, Sequencing, Polymerase Chain Reaction, Nested PCR, Molecular Weight

24) Product Images from "Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR"

Article Title: Simultaneous Use of MutS and RecA for Suppression of Nonspecific Amplification during PCR

Journal: Journal of Nucleic Acids

doi: 10.1155/2013/823730

The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.
Figure Legend Snippet: The error-suppressing effects of ttRecA and ttMutS in the presence of ATP. (a) A schematic representation for the mechanism by which ttMutS suppresses nonspecific amplifications during PCR. A ttMutS dimer recognizes mismatched bases generated by mishybridization of the primer and blocks the approach of DNA polymerase. (b) A schematic representation for the mechanism by which ttRecA suppresses nonspecific amplification during PCR. ttRecA promotes proper priming for PCR. (c) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0 to 0.4 mM ATP. Lanes 1–4, 5–8, and 9–12 are the results of the reaction without ttMutS or ttRecA, with 0.8 μ M ttMutS, and with 0.4 μ M ttRecA, respectively. The amounts of the amplified fragments were quantified by using the ImageJ software [ 9 ] and are shown as bar graphs in the lower panels, where gray and blue indicate nonspecific and desired amplifications, respectively. (d) A 423 bp region of the ttha1806 gene was amplified by using Takara LA Taq in the presence of 0.9, 2.7, 8.0, or 24 ng/mL template DNA ( T. thermophilus HB8 genomic DNA). The relative amounts of the amplified fragments are shown. Gray and blue bars indicate nonspecific and desired amplifications, respectively.

Techniques Used: Polymerase Chain Reaction, Generated, Amplification, Software

25) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

Techniques Used: Polymerase Chain Reaction, Sequencing

Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.
Figure Legend Snippet: Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.

Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Negative Control

26) Product Images from "Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes"

Article Title: Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes

Journal: Genetics

doi: 10.1534/genetics.108.094672

An Idaten transposon was trapped in the invA locus in mutant InvA4. (A–D) Young adults of four strains of V. carteri : (A) CRH22, the wild-type progenitor of all the mutants in this study; (B) strain InvA4; (C) strain InvA4R, a revertant derived
Figure Legend Snippet: An Idaten transposon was trapped in the invA locus in mutant InvA4. (A–D) Young adults of four strains of V. carteri : (A) CRH22, the wild-type progenitor of all the mutants in this study; (B) strain InvA4; (C) strain InvA4R, a revertant derived

Techniques Used: Mutagenesis, Derivative Assay

27) Product Images from "Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1 [C]Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1 [C] [W]Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1 [C] [W] [OA]"

Article Title: Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1 [C]Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1 [C] [W]Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication 1 [C] [W] [OA]

Journal: Plant Physiology

doi: 10.1104/pp.110.168500

Map-based cloning and identification of the Bh4 gene. A, The Bh4 locus was mapped in the interval of markers M1 and M2 on the long arm of chromosome 4 (Chr4). B, The Bh4 locus was further delimited to an 8.8-kb region between markers M5 and M7. C, Three
Figure Legend Snippet: Map-based cloning and identification of the Bh4 gene. A, The Bh4 locus was mapped in the interval of markers M1 and M2 on the long arm of chromosome 4 (Chr4). B, The Bh4 locus was further delimited to an 8.8-kb region between markers M5 and M7. C, Three

Techniques Used: Clone Assay

Multiple Independent Mutations of Bh4 in Rice Cultivars
Figure Legend Snippet: Multiple Independent Mutations of Bh4 in Rice Cultivars

Techniques Used:

Expression analysis of Bh4 . A, Transcripts of Bh4 and Actin1 detected by RT-PCR in root, stem, leaf, hull about 18 d after heading, and the corresponding dehulled seeds from Guangluai 4 (G) and NIL8 (N). B, qRT-PCR analysis of Bh4 transcripts in the hull
Figure Legend Snippet: Expression analysis of Bh4 . A, Transcripts of Bh4 and Actin1 detected by RT-PCR in root, stem, leaf, hull about 18 d after heading, and the corresponding dehulled seeds from Guangluai 4 (G) and NIL8 (N). B, qRT-PCR analysis of Bh4 transcripts in the hull

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

Sequence comparison of Bh4 and overexpression of Bh4 in Guangluai 4. A, Comparison of the Bh4 locus sequences from W1943, Guangluai 4, and Nipponbare. Sequence comparison of the Bh4 locus between W1943 and Guangluai 4 reveals a 22-bp deletion in the third
Figure Legend Snippet: Sequence comparison of Bh4 and overexpression of Bh4 in Guangluai 4. A, Comparison of the Bh4 locus sequences from W1943, Guangluai 4, and Nipponbare. Sequence comparison of the Bh4 locus between W1943 and Guangluai 4 reveals a 22-bp deletion in the third

Techniques Used: Sequencing, Over Expression

Phylogenetic Analysis of Bh4
Figure Legend Snippet: Phylogenetic Analysis of Bh4

Techniques Used:

Function prediction of Bh4 . A, Phylogenetic comparison of Bh4 with other amino acid transporters. A phylogenetic tree of Bh4 with other plant transporters was generated by MEGA 4.0. B, Prediction of the transmembrane domains of BH4 using the prediction
Figure Legend Snippet: Function prediction of Bh4 . A, Phylogenetic comparison of Bh4 with other amino acid transporters. A phylogenetic tree of Bh4 with other plant transporters was generated by MEGA 4.0. B, Prediction of the transmembrane domains of BH4 using the prediction

Techniques Used: Generated

Bh4 phylogeny of rice cultivars and wild relatives.
Figure Legend Snippet: Bh4 phylogeny of rice cultivars and wild relatives.

Techniques Used:

28) Product Images from "Establishment of nDart1-tagged lines of Koshihikari, an elite variety of rice in Japan"

Article Title: Establishment of nDart1-tagged lines of Koshihikari, an elite variety of rice in Japan

Journal: Breeding Science

doi: 10.1270/jsbbs.19049

Confirmation of nDart1-0 insertion revealed by TAIL-PCR. (A) GS (Green sector) and WS (White sector) in albino of Fig. 2B . (B) Banding pattern of WT, GS and WS using specific primers for each clone. White arrow and arrowhead indicate amplicons with nDart1 insertion and without nDart1 , respectively.
Figure Legend Snippet: Confirmation of nDart1-0 insertion revealed by TAIL-PCR. (A) GS (Green sector) and WS (White sector) in albino of Fig. 2B . (B) Banding pattern of WT, GS and WS using specific primers for each clone. White arrow and arrowhead indicate amplicons with nDart1 insertion and without nDart1 , respectively.

Techniques Used: Polymerase Chain Reaction

29) Product Images from "The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency"

Article Title: The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency

Journal: Nature Communications

doi: 10.1038/s41467-019-13110-8

Phylogenetic and functional analysis of OsNR2 haplotypes. a Phylogenetic tree of OsNR2 CDS from 222 accessions. Blue: O. sativa indica ; red: O. sativa japonica ; green: O. rufipogon ; Tej: Temperate japonica ; Trj: Tropical japonica . b Classification of 199 cultivated rice varieties according to haplotype (9311 versus Nipponbare) and extent of conferred ClO 3 - resistance (CR%). Error bars represent 95% confidence intervals. c DNA sequence diversity of the genomic region surrounding OsNR2 in three groups. The green, orange and blue lines indicate site nucleotide diversity (π) for O. rufipogon , O. sativa indica and O. sativa japonica accessions, respectively. The position of OsNR2 is as indicated (thick lines represent exons and thin lines introns). The source data underlying b are provided as a Source Data file
Figure Legend Snippet: Phylogenetic and functional analysis of OsNR2 haplotypes. a Phylogenetic tree of OsNR2 CDS from 222 accessions. Blue: O. sativa indica ; red: O. sativa japonica ; green: O. rufipogon ; Tej: Temperate japonica ; Trj: Tropical japonica . b Classification of 199 cultivated rice varieties according to haplotype (9311 versus Nipponbare) and extent of conferred ClO 3 - resistance (CR%). Error bars represent 95% confidence intervals. c DNA sequence diversity of the genomic region surrounding OsNR2 in three groups. The green, orange and blue lines indicate site nucleotide diversity (π) for O. rufipogon , O. sativa indica and O. sativa japonica accessions, respectively. The position of OsNR2 is as indicated (thick lines represent exons and thin lines introns). The source data underlying b are provided as a Source Data file

Techniques Used: Functional Assay, Sequencing

30) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

Techniques Used: Polymerase Chain Reaction, Sequencing

Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.
Figure Legend Snippet: Rickettsial gene-like sequences possibly located in the nuclear genomes of Volvox carteri strains. Schematic representations of arrangements/synteny (A-D) in, and semi-quantitative genomic PCR data (E) from, several rickettsial gene-like sequences possibly located in the nuclear genomes of V . carteri strains. Coding DNA sequence (CDS)-like regions are shown as boxes. Rickettsial CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates the gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Sequences including rickettsial CDS-like regions of V . carteri f. nagariensis strains UTEX 1886, NIES-397 and NIES-398. (B) Sequences including rickettsial gene homologs of V . carteri f. weismannia strains UTEX 1875 and UTEX 1876. Plus (+) indicates a frameshift deletion. (C) Sequence including rickettsial murB -like sequence of V . carteri f. weismannia strain UTEX 2170. (D) Sequences including rickettsial 16S rRNA gene-like sequences of V . carteri f. kawasakiensis NIES-732 and NIES-733. (E) Semi-quantitative genomic PCR of rickettsial genes and gene-like sequences. Each rickettsial gene-like sequence was amplified via genomic PCR using rickettsia-specific primer sets (see Materials and Methods ). The positions of primer sets with reference to target positions are shown in both Fig. 1 and this Fig. 2 . As a control, the actin gene was amplified. Chlamydomonas reinhardtii strain CC-503 was used as negative control.

Techniques Used: Polymerase Chain Reaction, Sequencing, Amplification, Negative Control

Phylogenetic positions of rickettsial 16S rRNA gene-like sequences in Volvox carteri nuclear genomes. The tree was inferred using the maximum-likelihood (ML) method based on 43 sequences and 1,403 nucleotides of the 16S rRNA genes from bacteria, endosymbionts (En) of eukaryotic hosts, and other environmental samples, of the family Rickettsiaceae , including rickettsial 16S rRNA gene-like sequences obtained from endosymbiont-lacking strains of V . carteri (bold). Bootstrap values (≥50%) for the ML and maximum parsimony analyses, and posterior probabilities (≥0.90) for Bayesian interference, are indicated at the respective nodes. The scale bar corresponds to 0.02 nucleotide substitutions per position. The hydra group and ‘ Candidatus Megaira polyxenophila’ refer to the organisms studied by Weinert et al. [ 10 ] and Schrallhammer et al. [ 9 ], respectively.
Figure Legend Snippet: Phylogenetic positions of rickettsial 16S rRNA gene-like sequences in Volvox carteri nuclear genomes. The tree was inferred using the maximum-likelihood (ML) method based on 43 sequences and 1,403 nucleotides of the 16S rRNA genes from bacteria, endosymbionts (En) of eukaryotic hosts, and other environmental samples, of the family Rickettsiaceae , including rickettsial 16S rRNA gene-like sequences obtained from endosymbiont-lacking strains of V . carteri (bold). Bootstrap values (≥50%) for the ML and maximum parsimony analyses, and posterior probabilities (≥0.90) for Bayesian interference, are indicated at the respective nodes. The scale bar corresponds to 0.02 nucleotide substitutions per position. The hydra group and ‘ Candidatus Megaira polyxenophila’ refer to the organisms studied by Weinert et al. [ 10 ] and Schrallhammer et al. [ 9 ], respectively.

Techniques Used: Environmental Sampling

Phylogenetic positions of rickettsial murB and ddlB gene-like sequences from endosymbiont-lacking strains of Volvox carteri . The tree was inferred using the maximum-likelihood (ML) method based on 637 amino acid sites in translated and combined murB and ddlB gene/gene-like sequences from 30 operational taxonomic units of bacteria in the Rickettsiaceae , including possible endosymbionts (En) of algal hosts, and possible nuclear-encoded sequences from endosymbiont-lacking strains of V . carteri (bold). Bootstrap values (≥50%) for ML and maximum parsimony analyses are indicated at the respective nodes. The scale bar corresponds to 0.1 amino acid substitutions per position.
Figure Legend Snippet: Phylogenetic positions of rickettsial murB and ddlB gene-like sequences from endosymbiont-lacking strains of Volvox carteri . The tree was inferred using the maximum-likelihood (ML) method based on 637 amino acid sites in translated and combined murB and ddlB gene/gene-like sequences from 30 operational taxonomic units of bacteria in the Rickettsiaceae , including possible endosymbionts (En) of algal hosts, and possible nuclear-encoded sequences from endosymbiont-lacking strains of V . carteri (bold). Bootstrap values (≥50%) for ML and maximum parsimony analyses are indicated at the respective nodes. The scale bar corresponds to 0.1 amino acid substitutions per position.

Techniques Used:

Phylogenetic relationships among 13 strains of three forms of Volvox carteri . The tree was inferred using the maximum-likelihood (ML) method based on alignment of 471 nucleotide sites in the internal transcribed spacer 2 sequences of 10 operational taxonomic units of V . carteri strains and V . obversus strain UTEX 1865 (the outgroup). Bootstrap values (50% or more) for the ML and maximum parsimony analyses are indicated at the respective nodes. The scale bar shows 0.05 nucleotide substitutions per position. The presence (+) or absence (-) of rickettsial endosymbionts based on the data of Kawafune et al. [ 12 ], and those of the present study ( S1 , S2 Figs.), are shown in the central column. Possible nuclear-encoded, rickettsial gene homologs detected in the present study ( Fig. 2E and S3 Fig. ) are shown in the column on the right. The gene names shown in bold were used in phylogenetic analyses (Figs. 3 , 4 and S4 , S5 Figs.). The letters A-D following gene names correspond to the forms of genetic composition shown in Fig. 2 . No rickettsial gene-like sequences were detected (in the present study) in strains UTEX 2903, UTEX 1874 or UTEX 2904.
Figure Legend Snippet: Phylogenetic relationships among 13 strains of three forms of Volvox carteri . The tree was inferred using the maximum-likelihood (ML) method based on alignment of 471 nucleotide sites in the internal transcribed spacer 2 sequences of 10 operational taxonomic units of V . carteri strains and V . obversus strain UTEX 1865 (the outgroup). Bootstrap values (50% or more) for the ML and maximum parsimony analyses are indicated at the respective nodes. The scale bar shows 0.05 nucleotide substitutions per position. The presence (+) or absence (-) of rickettsial endosymbionts based on the data of Kawafune et al. [ 12 ], and those of the present study ( S1 , S2 Figs.), are shown in the central column. Possible nuclear-encoded, rickettsial gene homologs detected in the present study ( Fig. 2E and S3 Fig. ) are shown in the column on the right. The gene names shown in bold were used in phylogenetic analyses (Figs. 3 , 4 and S4 , S5 Figs.). The letters A-D following gene names correspond to the forms of genetic composition shown in Fig. 2 . No rickettsial gene-like sequences were detected (in the present study) in strains UTEX 2903, UTEX 1874 or UTEX 2904.

Techniques Used:

31) Product Images from "One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)"

Article Title: One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)

Journal: BMC Genomics

doi: 10.1186/s12864-015-1432-5

Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .
Figure Legend Snippet: Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .

Techniques Used: Injection, Polymerase Chain Reaction, Nested PCR, Derivative Assay, Fluorescence

32) Product Images from "One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)"

Article Title: One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)

Journal: BMC Genomics

doi: 10.1186/s12864-015-1432-5

Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .
Figure Legend Snippet: Production of multiple targeted Tg mouse lines using i- PITT. (A) Schematic of simultaneous production of multiple Tg lines using i- PITT. Multiple donor vectors that harbor different DOI are mixed and co-injected with iCre and PhiC31o mRNA into the fertilized eggs carrying the i- PITT landing pad in their genome. Appearance of different fluorescent colors indicates successful insertion of DOI. (B) Schematic of targeted insertion alleles for each DOI. TI ex allele 1 is shown as an example. Arrows indicate the PCR primer sets used for genotype identification of the correct insertion. For detecting targeted transgenesis in blastocyst, 1st PCR was performed using the outer most primer pair sets (black and blue or black and green or black and red arrows) and nested PCR using the internal primer pair sets (purple arrows). For detecting targeted transgenesis in fetuses, PCR with only the purple primer pair is sufficient. (C) Example of simultaneous production of multiple targeted Tgs. Blastocysts (left panel) and day 13.5 fetuses (right panel) derived from injected zygotes. Zygotes/fetuses exhibiting blue, green or red fluorescence indicate successful insertion of DOI from pBGV, pBGW or pBDR vectors respectively. The results of PCR-based genotyping are shown below the images; arrows indicate positive samples. (D, E) The results of i- PITT experiment in blastocyst embryos (D) and fetuses/pups (E) .

Techniques Used: Injection, Polymerase Chain Reaction, Nested PCR, Derivative Assay, Fluorescence

33) Product Images from "Duplex fluorescence melting curve analysis as a new tool for rapid detection and differentiation of genotype I, II and Bartha-K61 vaccine strains of pseudorabies virus"

Article Title: Duplex fluorescence melting curve analysis as a new tool for rapid detection and differentiation of genotype I, II and Bartha-K61 vaccine strains of pseudorabies virus

Journal: BMC Veterinary Research

doi: 10.1186/s12917-018-1697-4

Schematic illustration of the duplex FMCA method. ( a ) Relative binding positions of primers and probes along the gC gene of PRV. Melting peak calculation by derivative plotting -dF/dT versus temperature in the FAM channel ( b ) and the HEX channel ( c ). Red, blue, and green lines represent Bartha-K61 vaccine, European/American (Genotype I), and Chinese (Genotype II) strains, respectively
Figure Legend Snippet: Schematic illustration of the duplex FMCA method. ( a ) Relative binding positions of primers and probes along the gC gene of PRV. Melting peak calculation by derivative plotting -dF/dT versus temperature in the FAM channel ( b ) and the HEX channel ( c ). Red, blue, and green lines represent Bartha-K61 vaccine, European/American (Genotype I), and Chinese (Genotype II) strains, respectively

Techniques Used: Binding Assay

34) Product Images from "Exome sequencing reveals a novel MFN2 missense mutation in a Chinese family with Charcot-Marie-Tooth type 2A"

Article Title: Exome sequencing reveals a novel MFN2 missense mutation in a Chinese family with Charcot-Marie-Tooth type 2A

Journal: Experimental and Therapeutic Medicine

doi: 10.3892/etm.2018.6513

Identification of a missense mutation in the MFN2 gene. (A) The novel mutation c.1190G > C; p.(R397P) was verified by Sanger sequencing. (B) PCR-restriction fragment length polymorphism suggested the phenotype and genotype co-segregation in this pedigree. The nested PCR products of the affected family members (II3, II6, III2, III3, III4, III5 and IV1) were digested into two fragments (107 and 86 bp) by MSPI and the others were not affected. (C) Multi-species sequence alignment showing the evolutionarily conserved p.R397 position in MFN2. MFN2, mitofusin 2; PCR, polymerase chain reaction; M, molecular weight standards (50 bp DNA Ladder).
Figure Legend Snippet: Identification of a missense mutation in the MFN2 gene. (A) The novel mutation c.1190G > C; p.(R397P) was verified by Sanger sequencing. (B) PCR-restriction fragment length polymorphism suggested the phenotype and genotype co-segregation in this pedigree. The nested PCR products of the affected family members (II3, II6, III2, III3, III4, III5 and IV1) were digested into two fragments (107 and 86 bp) by MSPI and the others were not affected. (C) Multi-species sequence alignment showing the evolutionarily conserved p.R397 position in MFN2. MFN2, mitofusin 2; PCR, polymerase chain reaction; M, molecular weight standards (50 bp DNA Ladder).

Techniques Used: Mutagenesis, Sequencing, Polymerase Chain Reaction, Nested PCR, Molecular Weight

35) Product Images from "The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency"

Article Title: The indica nitrate reductase gene OsNR2 allele enhances rice yield potential and nitrogen use efficiency

Journal: Nature Communications

doi: 10.1038/s41467-019-13110-8

An Arg-Trp amino acid substitution reduces the specific activity of Nipponbare OsNR2. a Amino acid substitution and insertion differences between the 9311 and Nipponbare OsNR2 proteins. Locations of conserved functional domains are indicated by green bars. b Constructs expressing chimeric OsNR2 proteins of varying amino acid sequence. Fragments from the 9311 and Nipponbare OsNR2 coding regions were exchanged to generate constructs encoding a series of four different chimeric OsNR2 proteins, differing with respect to the amino acid residues variant between 9311 and Nipponbare OsNR2. These constructs were expressed in E.coli . c Detection with anti:GST antibody (Cat No: CW0084M, CWBIOtech, Beijing, China) of OsNR2-GST fusion proteins extracted from E. coli and purified on a GST-sefinose TM column (constructs as shown in b ), showing roughly equivalent abundance of OsNR2 proteins. d NR activity of purified extracts as in b , c . Value is mean ± s.d. ( n = 3). Error bar represents s.d. ** indicates the least significant difference at 0.01 probability level compared with Nipponbare. The source data underlying c and d are provided as a Source Data file
Figure Legend Snippet: An Arg-Trp amino acid substitution reduces the specific activity of Nipponbare OsNR2. a Amino acid substitution and insertion differences between the 9311 and Nipponbare OsNR2 proteins. Locations of conserved functional domains are indicated by green bars. b Constructs expressing chimeric OsNR2 proteins of varying amino acid sequence. Fragments from the 9311 and Nipponbare OsNR2 coding regions were exchanged to generate constructs encoding a series of four different chimeric OsNR2 proteins, differing with respect to the amino acid residues variant between 9311 and Nipponbare OsNR2. These constructs were expressed in E.coli . c Detection with anti:GST antibody (Cat No: CW0084M, CWBIOtech, Beijing, China) of OsNR2-GST fusion proteins extracted from E. coli and purified on a GST-sefinose TM column (constructs as shown in b ), showing roughly equivalent abundance of OsNR2 proteins. d NR activity of purified extracts as in b , c . Value is mean ± s.d. ( n = 3). Error bar represents s.d. ** indicates the least significant difference at 0.01 probability level compared with Nipponbare. The source data underlying c and d are provided as a Source Data file

Techniques Used: Activity Assay, Functional Assay, Construct, Expressing, Sequencing, Variant Assay, Purification

Expression of the 9311 OsNR2 allele boosts Nipponbare N assimilation, tiller number, and grain yield. a effective tiller number, b yield per plant and c yield per plot of Nipponbare, Nipponbare harboring constructs for expression of the 9311 OsNR2 allele driven by the 9311 OsNR2 promoter ( OsNR2 -9311-1 and OsNR2 -9311-2) or of OsNR2 RNAi ( OsNR2- RNAi-1 and OsNR2- RNAi-2). d NR active activity of Nipponbare (empty-vector control; EV), transgenic derivatives expressing the 9311 OsNR2 allele (9311-1 and 9311-2), and transgenic derivatives expressing the Nipponbare OsNR2 allele (NPB-1 and NPB-2), with expression of both alleles being driven by the CaMV 35S promoter. e 15 NO 3 - uptake of plants exposed to 1.25 mM 15 NO 3 , f N content of aboveground plant parts, g panicle N content, h effective tiller number, i yield per plant, j yield per plot and k appearance of plant genotypes (as in ( d )). Plants were cultivated in field conditions with NO 3 − fertilizer (14 kg per acre) as major N source f – i . Values are mean ± s.d. ( n = 6 for a - b , f – i , n = 3 for d , e and n = 2 for c , j ). Error bar represents s.d. * and ** respectively indicate least significant differences at the 0.05 and 0.01 probability levels, compared with Nipponbare or EV. HZ: Hangzhou (harvested on September 20th, 2018); HN: Hainan (harvested on April 20th, 2019). Source data are provided as a Source Data file
Figure Legend Snippet: Expression of the 9311 OsNR2 allele boosts Nipponbare N assimilation, tiller number, and grain yield. a effective tiller number, b yield per plant and c yield per plot of Nipponbare, Nipponbare harboring constructs for expression of the 9311 OsNR2 allele driven by the 9311 OsNR2 promoter ( OsNR2 -9311-1 and OsNR2 -9311-2) or of OsNR2 RNAi ( OsNR2- RNAi-1 and OsNR2- RNAi-2). d NR active activity of Nipponbare (empty-vector control; EV), transgenic derivatives expressing the 9311 OsNR2 allele (9311-1 and 9311-2), and transgenic derivatives expressing the Nipponbare OsNR2 allele (NPB-1 and NPB-2), with expression of both alleles being driven by the CaMV 35S promoter. e 15 NO 3 - uptake of plants exposed to 1.25 mM 15 NO 3 , f N content of aboveground plant parts, g panicle N content, h effective tiller number, i yield per plant, j yield per plot and k appearance of plant genotypes (as in ( d )). Plants were cultivated in field conditions with NO 3 − fertilizer (14 kg per acre) as major N source f – i . Values are mean ± s.d. ( n = 6 for a - b , f – i , n = 3 for d , e and n = 2 for c , j ). Error bar represents s.d. * and ** respectively indicate least significant differences at the 0.05 and 0.01 probability levels, compared with Nipponbare or EV. HZ: Hangzhou (harvested on September 20th, 2018); HN: Hainan (harvested on April 20th, 2019). Source data are provided as a Source Data file

Techniques Used: Expressing, Construct, Activity Assay, Plasmid Preparation, Transgenic Assay

Phylogenetic and functional analysis of OsNR2 haplotypes. a Phylogenetic tree of OsNR2 CDS from 222 accessions. Blue: O. sativa indica ; red: O. sativa japonica ; green: O. rufipogon ; Tej: Temperate japonica ; Trj: Tropical japonica . b Classification of 199 cultivated rice varieties according to haplotype (9311 versus Nipponbare) and extent of conferred ClO 3 - resistance (CR%). Error bars represent 95% confidence intervals. c DNA sequence diversity of the genomic region surrounding OsNR2 in three groups. The green, orange and blue lines indicate site nucleotide diversity (π) for O. rufipogon , O. sativa indica and O. sativa japonica accessions, respectively. The position of OsNR2 is as indicated (thick lines represent exons and thin lines introns). The source data underlying b are provided as a Source Data file
Figure Legend Snippet: Phylogenetic and functional analysis of OsNR2 haplotypes. a Phylogenetic tree of OsNR2 CDS from 222 accessions. Blue: O. sativa indica ; red: O. sativa japonica ; green: O. rufipogon ; Tej: Temperate japonica ; Trj: Tropical japonica . b Classification of 199 cultivated rice varieties according to haplotype (9311 versus Nipponbare) and extent of conferred ClO 3 - resistance (CR%). Error bars represent 95% confidence intervals. c DNA sequence diversity of the genomic region surrounding OsNR2 in three groups. The green, orange and blue lines indicate site nucleotide diversity (π) for O. rufipogon , O. sativa indica and O. sativa japonica accessions, respectively. The position of OsNR2 is as indicated (thick lines represent exons and thin lines introns). The source data underlying b are provided as a Source Data file

Techniques Used: Functional Assay, Sequencing

OsNR2 allelic variation confers the qCR2 , and affects NR active activity and 15 NO 3 - uptake. a ClO 3 − resistance (CR) QTL analysis of RILs from an indica (9311) × japonica (Nipponbare) cross, performed on seedlings germinated from seeds harvested in Hangzhou or Hainan (see Methods). Major QTLs are shown, with numbers indicating genetic map position (cM) on each chromosome. b Fine mapping of qCR2 with a residual heterozygote line (RHL) F 2 population. Using a panel of linked markers (Supplementary Table 2 ), qCR2 was pin-pointed to a 6.4 kb region (Chr.2, between markers IND2-3 and IND2-5) containing OsNR2 . Numbers of recombinants between each marker and qCR2 are shown. OsNR2 structure is shown, black boxes represent exons. c Relative seedling vigor indicates degree of ClO 3 − resistance (Nipponbare harboring constructs for expression of the 9311 OsNR2 allele driven by the 9311 OsNR2 promoter ( OsNR2 -9311-1 and OsNR2 -9311-2) or of OsNR2 RNAi ( OsNR2- RNAi-1 and OsNR2- RNAi-2); see Supplementary Fig. 1 ). d Leaf OsNR2 mRNA abundance, e leaf NR active activity, f 15 NO 3 − uptake activity of roots exposed to 1.25 mM 15 NO 3 − . Value is mean ± s.d. ( n = 3 for d – f ). Error bar represents s.d. * and ** respectively indicate least significant differences at the 0.05 and 0.01 probability level compared with Nipponbare. The source data underlying Fig. 1d–f are provided as a Source Data file
Figure Legend Snippet: OsNR2 allelic variation confers the qCR2 , and affects NR active activity and 15 NO 3 - uptake. a ClO 3 − resistance (CR) QTL analysis of RILs from an indica (9311) × japonica (Nipponbare) cross, performed on seedlings germinated from seeds harvested in Hangzhou or Hainan (see Methods). Major QTLs are shown, with numbers indicating genetic map position (cM) on each chromosome. b Fine mapping of qCR2 with a residual heterozygote line (RHL) F 2 population. Using a panel of linked markers (Supplementary Table 2 ), qCR2 was pin-pointed to a 6.4 kb region (Chr.2, between markers IND2-3 and IND2-5) containing OsNR2 . Numbers of recombinants between each marker and qCR2 are shown. OsNR2 structure is shown, black boxes represent exons. c Relative seedling vigor indicates degree of ClO 3 − resistance (Nipponbare harboring constructs for expression of the 9311 OsNR2 allele driven by the 9311 OsNR2 promoter ( OsNR2 -9311-1 and OsNR2 -9311-2) or of OsNR2 RNAi ( OsNR2- RNAi-1 and OsNR2- RNAi-2); see Supplementary Fig. 1 ). d Leaf OsNR2 mRNA abundance, e leaf NR active activity, f 15 NO 3 − uptake activity of roots exposed to 1.25 mM 15 NO 3 − . Value is mean ± s.d. ( n = 3 for d – f ). Error bar represents s.d. * and ** respectively indicate least significant differences at the 0.05 and 0.01 probability level compared with Nipponbare. The source data underlying Fig. 1d–f are provided as a Source Data file

Techniques Used: Activity Assay, Marker, Construct, Expressing

OsNR2 and OsNRT1.1B interact to promote rice yield and NUE. a root OsNRT1.1B mRNA abundance, b leaf OsNR2 mRNA abundance, c leaf NR active activity, d 15 NO 3 − uptake activity of roots exposed to 1.25 mM 15 NO 3 − , e effective tiller number, f yield per plant, g yield per plot and h NUE of Nipponbare, NIL- qCR2 , NIL- qCR10 and NIL- qCR2/qCR10 . Values are mean ± s.d. ( n = 3 for a – d , n = 6 for e , f , h and n = 2 for g ). Error bar represents s.d. Plants cultivated in field conditions with NO 3 − fertilizer (14 kg per acre) as major N source e – h . * and ** respectively indicate least significant differences at the 0.05 and 0.01 probability levels, compared with Nipponbare. HZ: Hangzhou (harvested on September 20th, 2018); HN: Hainan (harvested on April 20th, 2019). Source data are provided as a Source Data file
Figure Legend Snippet: OsNR2 and OsNRT1.1B interact to promote rice yield and NUE. a root OsNRT1.1B mRNA abundance, b leaf OsNR2 mRNA abundance, c leaf NR active activity, d 15 NO 3 − uptake activity of roots exposed to 1.25 mM 15 NO 3 − , e effective tiller number, f yield per plant, g yield per plot and h NUE of Nipponbare, NIL- qCR2 , NIL- qCR10 and NIL- qCR2/qCR10 . Values are mean ± s.d. ( n = 3 for a – d , n = 6 for e , f , h and n = 2 for g ). Error bar represents s.d. Plants cultivated in field conditions with NO 3 − fertilizer (14 kg per acre) as major N source e – h . * and ** respectively indicate least significant differences at the 0.05 and 0.01 probability levels, compared with Nipponbare. HZ: Hangzhou (harvested on September 20th, 2018); HN: Hainan (harvested on April 20th, 2019). Source data are provided as a Source Data file

Techniques Used: Activity Assay

36) Product Images from "Two Different Rickettsial Bacteria Invading Volvox carteri"

Article Title: Two Different Rickettsial Bacteria Invading Volvox carteri

Journal: PLoS ONE

doi: 10.1371/journal.pone.0116192

Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).
Figure Legend Snippet: Rickettsial genes and gene-like sequences in the genomes of Volvox carteri and rickettsial possible endosymbionts. Schematic representations of arrangements/synteny of several rickettsial genes and gene-like sequences present in DNA of the nuclear genome of V . carteri (A) and in the genomes of rickettsial possible endosymbionts harbored by three volvocalean species (B-D). Coding DNA sequences (CDSs) and CDS-like regions are shown as boxes. Rickettsial CDSs/CDS-like regions are shown in pale yellow, the V . carteri transposon Jordan -like region in green and others in black. Placement of boxes above/below the line indicates gene direction (from left-to-right or right-to-left, respectively). Black double-headed arrows on the baseline indicate the regions sequenced in the present study. Colored triangles under boxes indicate the locations of primers used for semi-quantitative genomic PCR (16S rRNA gene 5′-region: magenta, 16S rRNA gene 3′-region: light blue, murB : orange, ddlB : green; Fig. 2E ). For accession numbers of sequences used in this figure, see S3 Table . (A) Part of scaffold 6 of the V . carteri f. nagariensis strain EVE nuclear genome. (B) Part of the Carteria cerasiformis NIES-425 draft endosymbiont genome, including 16S rRNA (first line) and murB - ftsQ (second line). White triangles indicate primers used to amplify the sequencing templates (ccmF-R02 and phbB-F01; see Materials and Methods ). (C) Part of the genome of a possible endosymbiont of V . carteri f. weismannia strain UTEX 2180, including murB and ddlB (right). The 16S rRNA gene of the endosymbiont [ 12 ] is also shown (left). (D) Part of the genome of a possible endosymbiont of Pleodorina japonica strain NIES-577, including murB and ddlB (right). The 16S rRNA gene [ 11 ] is also shown (left).

Techniques Used: Polymerase Chain Reaction, Sequencing

37) Product Images from "Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain"

Article Title: Curing the Megaplasmid pTT27 from Thermus thermophilus HB27 and Maintaining Exogenous Plasmids in the Plasmid-Free Strain

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.03603-15

Minimum replicon of pTT27.
Figure Legend Snippet: Minimum replicon of pTT27.

Techniques Used:

Minimization of pTT27 in a stepwise manner. (A) Scheme for the stepwise deletions. The plasmids were constructed in E. coli , and replication ability was confirmed by transformation of the recA -null mutant of HB27. The top line indicates the pUC27H4 from
Figure Legend Snippet: Minimization of pTT27 in a stepwise manner. (A) Scheme for the stepwise deletions. The plasmids were constructed in E. coli , and replication ability was confirmed by transformation of the recA -null mutant of HB27. The top line indicates the pUC27H4 from

Techniques Used: Construct, Transformation Assay, Mutagenesis

Curing pTT27 from T. thermophilus HB27. (A) Strategy to cure the pTT27 megaplasmid from HB27. When HB27 was transformed by pUC27H11, the intact pTT27 was excluded due to plasmid incompatibility. The transformant lacking pTT27 but containing pUC27H11 was
Figure Legend Snippet: Curing pTT27 from T. thermophilus HB27. (A) Strategy to cure the pTT27 megaplasmid from HB27. When HB27 was transformed by pUC27H11, the intact pTT27 was excluded due to plasmid incompatibility. The transformant lacking pTT27 but containing pUC27H11 was

Techniques Used: Transformation Assay, Plasmid Preparation

RNR can function in pTT27 replication in trans . To test whether the RNR acts in the megaplasmid replication in trans , the transposase-encoding TT_C0665 gene on the chromosome of the PFW strain was replaced by the RNR genes with Bm r for the selection marker,
Figure Legend Snippet: RNR can function in pTT27 replication in trans . To test whether the RNR acts in the megaplasmid replication in trans , the transposase-encoding TT_C0665 gene on the chromosome of the PFW strain was replaced by the RNR genes with Bm r for the selection marker,

Techniques Used: Selection, Marker

Gel retardation assay to identify the RepT-binding region. (A) The fragmented pTT27 regions of pUC27H11 were incubated with the recombinant RepT protein at 0, 0.37, 0.74, and 1.5 μM (lanes 1 to 4, respectively), and the RepT-binding region was
Figure Legend Snippet: Gel retardation assay to identify the RepT-binding region. (A) The fragmented pTT27 regions of pUC27H11 were incubated with the recombinant RepT protein at 0, 0.37, 0.74, and 1.5 μM (lanes 1 to 4, respectively), and the RepT-binding region was

Techniques Used: Electrophoretic Mobility Shift Assay, Binding Assay, Incubation, Recombinant

Initial deletion of pTT27 region in HB27.
Figure Legend Snippet: Initial deletion of pTT27 region in HB27.

Techniques Used:

Large-scale deletion in megaplasmid pTT27. (A) Deletion approaches used in this study. Panel i, two PCR-amplified 5-kbp fragments, represented by the arrows, were inserted into pUC-Hm as a homologous region for recombination (dotted lines) with pTT27.
Figure Legend Snippet: Large-scale deletion in megaplasmid pTT27. (A) Deletion approaches used in this study. Panel i, two PCR-amplified 5-kbp fragments, represented by the arrows, were inserted into pUC-Hm as a homologous region for recombination (dotted lines) with pTT27.

Techniques Used: Polymerase Chain Reaction, Amplification

Stepwise deletions in the pTT27 megaplasmid.
Figure Legend Snippet: Stepwise deletions in the pTT27 megaplasmid.

Techniques Used:

38) Product Images from "Involvement of MAFB and MAFF in Retinoid-Mediated Suppression of Hepatocellular Carcinoma Invasion"

Article Title: Involvement of MAFB and MAFF in Retinoid-Mediated Suppression of Hepatocellular Carcinoma Invasion

Journal: International Journal of Molecular Sciences

doi: 10.3390/ijms19051450

Gene expression in different types of liver diseases. Box and whisker plots of relative gene expression levels of TFPI2, RARα, RARβ, MAFB, and MAFF to β-actin in normal (N, n = 8; blue), fatty (FL, n = 5; green), hepatitis (Hs, n = 3; yellow), cirrhotic (Cir, n = 5; orange), and hepatocellular carcinoma (Tu, n = 23; red) liver tissues. Boxes indicate first and third quartiles and median values and whiskers represent 5 and 95 percentiles. Open circulars indicate outliers. * p
Figure Legend Snippet: Gene expression in different types of liver diseases. Box and whisker plots of relative gene expression levels of TFPI2, RARα, RARβ, MAFB, and MAFF to β-actin in normal (N, n = 8; blue), fatty (FL, n = 5; green), hepatitis (Hs, n = 3; yellow), cirrhotic (Cir, n = 5; orange), and hepatocellular carcinoma (Tu, n = 23; red) liver tissues. Boxes indicate first and third quartiles and median values and whiskers represent 5 and 95 percentiles. Open circulars indicate outliers. * p

Techniques Used: Expressing, Whisker Assay

ATRA-induced TFPI2 expression in HuH7 cells. ( A ) Dose-dependent expression of TFPI2 (red) and RARβ (blue) mRNA in HuH7 ( left ) and HepG2 ( right ) cells following incubation with ATRA for 12 h ( n = 4). * p
Figure Legend Snippet: ATRA-induced TFPI2 expression in HuH7 cells. ( A ) Dose-dependent expression of TFPI2 (red) and RARβ (blue) mRNA in HuH7 ( left ) and HepG2 ( right ) cells following incubation with ATRA for 12 h ( n = 4). * p

Techniques Used: Expressing, Incubation

Abrogation of the suppressive effect of ATRA on HuH7 cell invasion by TFPI2 knockdown. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shTFPI2-1, and shTFPI2-2 (NT, T2KD-1, and T2KD-2 cells, respectively). The cells were treated with EtOH (blue) and 2 µM ATRA (red) for 12 h ( n = 4). * p
Figure Legend Snippet: Abrogation of the suppressive effect of ATRA on HuH7 cell invasion by TFPI2 knockdown. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shTFPI2-1, and shTFPI2-2 (NT, T2KD-1, and T2KD-2 cells, respectively). The cells were treated with EtOH (blue) and 2 µM ATRA (red) for 12 h ( n = 4). * p

Techniques Used: Expressing, Stable Transfection, Transfection

Kaplan–Meier analyses of disease-free survival of HCC patients from the TCGA cohort. ( A , B ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFB expression in HCC with higher TFPI2 ( n = 68 or n = 93, respectively) ( A ) or higher MAFF ( n = 83 or 70, respectively) ( B ) groups, ( C , D ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFF expression in HCC with lower TFPI2 ( n = 94 or n = 62, respectively) ( C ) or lower MAFB ( n = 73 or n = 83, respectively) ( D ) groups. P values shown were calculated by log-rank test. Median values of gene expression were used to divide the patients into the higher or lower groups.
Figure Legend Snippet: Kaplan–Meier analyses of disease-free survival of HCC patients from the TCGA cohort. ( A , B ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFB expression in HCC with higher TFPI2 ( n = 68 or n = 93, respectively) ( A ) or higher MAFF ( n = 83 or 70, respectively) ( B ) groups, ( C , D ) Disease-free survival curves of patients with lower (blue) or higher (red) MAFF expression in HCC with lower TFPI2 ( n = 94 or n = 62, respectively) ( C ) or lower MAFB ( n = 73 or n = 83, respectively) ( D ) groups. P values shown were calculated by log-rank test. Median values of gene expression were used to divide the patients into the higher or lower groups.

Techniques Used: Expressing

Transcriptional regulation of TFPI2 expression by ATRA in HuH7 cells. ( A , B ) HuH7 ( A ) and HepG2 ( B ) cells pre-treated with ActD incubated with EtOH (blue) and 2 µM ATRA (red) for the indicated times. Left, RARβ, right, TFPI2 ( n = 4); ( C ) HuH7 and HepG2 cells pre-treated with N -hydroxy- N ′-phenyloctanediamide (SAHA) (blue) and AzC (red) incubated with EtOH and 2 µM ATRA for 12 h. RARβ ( Left ), TFPI2 ( right ) ( n = 4). * p
Figure Legend Snippet: Transcriptional regulation of TFPI2 expression by ATRA in HuH7 cells. ( A , B ) HuH7 ( A ) and HepG2 ( B ) cells pre-treated with ActD incubated with EtOH (blue) and 2 µM ATRA (red) for the indicated times. Left, RARβ, right, TFPI2 ( n = 4); ( C ) HuH7 and HepG2 cells pre-treated with N -hydroxy- N ′-phenyloctanediamide (SAHA) (blue) and AzC (red) incubated with EtOH and 2 µM ATRA for 12 h. RARβ ( Left ), TFPI2 ( right ) ( n = 4). * p

Techniques Used: Expressing, Incubation

Regulation of human TFPI2 promoter by RARα, MAFB, and MAFF. ( A , B ) A luciferase reporter vector driven by the human TFPI2 promoter was transfected along with pDNA expressing the indicated transcription factor genes with ( B ) and without ( A ) RARα-pDNA into HuH7 cells ( n = 4). Twenty-four hours after transfection, EtOH (blue) and 2 µM ATRA (red) were added to the cells, and further incubated for 24 h, which was followed by dual luciferase assay. * p
Figure Legend Snippet: Regulation of human TFPI2 promoter by RARα, MAFB, and MAFF. ( A , B ) A luciferase reporter vector driven by the human TFPI2 promoter was transfected along with pDNA expressing the indicated transcription factor genes with ( B ) and without ( A ) RARα-pDNA into HuH7 cells ( n = 4). Twenty-four hours after transfection, EtOH (blue) and 2 µM ATRA (red) were added to the cells, and further incubated for 24 h, which was followed by dual luciferase assay. * p

Techniques Used: Luciferase, Plasmid Preparation, Transfection, Expressing, Incubation

Effect of RARα, MAFB, and MAFF on HuH7 cell invasion through TFPI2. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shRARα, shMAFB, or shMAFF (NT, RaKD, MBKD, and MFKD cells, respectively). The cells were treated with EtOH (blue) or 2 µM ATRA (red) for 12 h ( n = 4). * p
Figure Legend Snippet: Effect of RARα, MAFB, and MAFF on HuH7 cell invasion through TFPI2. ( A ) TFPI2 mRNA expression in HuH7 cells stably transfected with shNT, shRARα, shMAFB, or shMAFF (NT, RaKD, MBKD, and MFKD cells, respectively). The cells were treated with EtOH (blue) or 2 µM ATRA (red) for 12 h ( n = 4). * p

Techniques Used: Expressing, Stable Transfection, Transfection

39) Product Images from "Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes"

Article Title: Idaten Is a New Cold-Inducible Transposon of Volvox carteri That Can Be Used for Tagging Developmentally Important Genes

Journal: Genetics

doi: 10.1534/genetics.108.094672

Transposon tagging with Idaten-2 . (A) A young adult of the “fully inversionless” mutant, InvC1; note gonidia that are exposed on the outside. Bar, 100 μm. (B) A young adult of InvC1R, a revertant strain derived from InvC; note
Figure Legend Snippet: Transposon tagging with Idaten-2 . (A) A young adult of the “fully inversionless” mutant, InvC1; note gonidia that are exposed on the outside. Bar, 100 μm. (B) A young adult of InvC1R, a revertant strain derived from InvC; note

Techniques Used: Mutagenesis, Derivative Assay

Structure of Idaten . (A) Schematic maps of Idaten and Idaten-2 . The pair of solid triangles at opposite ends represent the terminal inverted repeats (TIRs). Both elements contain repetitive regions (striped boxes). Repetitive region I is enriched in C
Figure Legend Snippet: Structure of Idaten . (A) Schematic maps of Idaten and Idaten-2 . The pair of solid triangles at opposite ends represent the terminal inverted repeats (TIRs). Both elements contain repetitive regions (striped boxes). Repetitive region I is enriched in C

Techniques Used:

Modifications of target-site sequences that are associated with insertion and excision of Idaten and Idaten-2 . The 3-bp TSDs are shown in boldface type. Open rectangles with closed triangles at their ends represent Idaten or Idaten-2 inserts. In the revertants,
Figure Legend Snippet: Modifications of target-site sequences that are associated with insertion and excision of Idaten and Idaten-2 . The 3-bp TSDs are shown in boldface type. Open rectangles with closed triangles at their ends represent Idaten or Idaten-2 inserts. In the revertants,

Techniques Used:

Related Articles

Nucleic Acid Electrophoresis:

Article Title: Behavior of DNA fibers stretched by precise meniscus motion control
Article Snippet: .. Total Thermus thermophilus HB8 genomic DNA (code no. 3071; Takara Shuzo, Japan), which was confirmed to contain > 20 kb DNA by electrophoresis, was suspended at 203 µg/ml in TE. .. A working solution was prepared (10 µl) containing 4 ng/µl DNA fragments and 0.1 µM YOYO-1 in TE.

Amplification:

Article Title: Purification, crystallization and preliminary X-ray diffraction of SecDF, a translocon-associated membrane protein, from Thermus thermophilus
Article Snippet: .. The secDF gene (gene ID 3168575) was amplified from T. thermophilus HB8 genomic DNA (purchased from Takara Shuzo), using Pfx DNA polymerase (Invitrogen) and primers 5′-CTG CCATG G ACCGGAAAAACCTCACCAG-3′ and 5′-GAC GGTACC CTA ATGGTGATGGTGATGGTG GGCCTTGCTGGCCTCTTGG-3′. .. The upstream primer contained the Nco I-recognition sequence (in italics in the first sequence) to enable in-frame fusion of the TSecDF-coding region to the second codon of lacZ α on the cloning vector which also contained the Nco I site.

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