Structured Review

Roche digoxigenin
Analysis of MAT1-2-1 copy number using Southern blotting. 8A) Gene diagrams of Sclerotinia sclerotiorum Inv- (left) and Inv+ (right) MAT loci illustrating the positions of the Southern probe with respect to the restriction sites used for Southern analyses. Boxes represent genes, white and dotted boxes correspond to alpha1 and HMG domains, respectively, dashed box represents MAT1-1-1 3’-fragment lacking an in frame start codon. Gene names are indicated above or within the boxes. The positions of the Bsa HI restriction sites (black triangles) and the distances between the Bsa HI sites are indicated above the boxes. The position of the Southern probe is marked by a horizontal black line beneath MAT1-2-1. The Inv+ alpha1 box is truncated after 45 bp and is not illustrated, for details see text. 8B) Southern blot of Bsa HI-digested genomic DNA visualized with the <t>digoxigenin-labeled</t> MAT1-2-1 specific probe. Wells 1 - 8 correspond to S. sclerotiorum strains 1B331-1 – 1B331-8 that represent an ordered tetrad, band sizes are indicated on the right. Lanes 1, 2, 5 and 6 have the pattern reflective of an Inv+ MAT locus, lanes 3, 4, 7 and 8 have the pattern expected for an Inv- MAT locus.
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Images

1) Product Images from "The Sclerotinia sclerotiorum Mating Type Locus (MAT) Contains a 3.6-kb Region That Is Inverted in Every Meiotic Generation"

Article Title: The Sclerotinia sclerotiorum Mating Type Locus (MAT) Contains a 3.6-kb Region That Is Inverted in Every Meiotic Generation

Journal: PLoS ONE

doi: 10.1371/journal.pone.0056895

Analysis of MAT1-2-1 copy number using Southern blotting. 8A) Gene diagrams of Sclerotinia sclerotiorum Inv- (left) and Inv+ (right) MAT loci illustrating the positions of the Southern probe with respect to the restriction sites used for Southern analyses. Boxes represent genes, white and dotted boxes correspond to alpha1 and HMG domains, respectively, dashed box represents MAT1-1-1 3’-fragment lacking an in frame start codon. Gene names are indicated above or within the boxes. The positions of the Bsa HI restriction sites (black triangles) and the distances between the Bsa HI sites are indicated above the boxes. The position of the Southern probe is marked by a horizontal black line beneath MAT1-2-1. The Inv+ alpha1 box is truncated after 45 bp and is not illustrated, for details see text. 8B) Southern blot of Bsa HI-digested genomic DNA visualized with the digoxigenin-labeled MAT1-2-1 specific probe. Wells 1 - 8 correspond to S. sclerotiorum strains 1B331-1 – 1B331-8 that represent an ordered tetrad, band sizes are indicated on the right. Lanes 1, 2, 5 and 6 have the pattern reflective of an Inv+ MAT locus, lanes 3, 4, 7 and 8 have the pattern expected for an Inv- MAT locus.
Figure Legend Snippet: Analysis of MAT1-2-1 copy number using Southern blotting. 8A) Gene diagrams of Sclerotinia sclerotiorum Inv- (left) and Inv+ (right) MAT loci illustrating the positions of the Southern probe with respect to the restriction sites used for Southern analyses. Boxes represent genes, white and dotted boxes correspond to alpha1 and HMG domains, respectively, dashed box represents MAT1-1-1 3’-fragment lacking an in frame start codon. Gene names are indicated above or within the boxes. The positions of the Bsa HI restriction sites (black triangles) and the distances between the Bsa HI sites are indicated above the boxes. The position of the Southern probe is marked by a horizontal black line beneath MAT1-2-1. The Inv+ alpha1 box is truncated after 45 bp and is not illustrated, for details see text. 8B) Southern blot of Bsa HI-digested genomic DNA visualized with the digoxigenin-labeled MAT1-2-1 specific probe. Wells 1 - 8 correspond to S. sclerotiorum strains 1B331-1 – 1B331-8 that represent an ordered tetrad, band sizes are indicated on the right. Lanes 1, 2, 5 and 6 have the pattern reflective of an Inv+ MAT locus, lanes 3, 4, 7 and 8 have the pattern expected for an Inv- MAT locus.

Techniques Used: Southern Blot, Labeling

2) Product Images from "Identification of Functional mob Regions in Rhizobium etli: Evidence for Self-Transmissibility of the Symbiotic Plasmid pRetCFN42d"

Article Title: Identification of Functional mob Regions in Rhizobium etli: Evidence for Self-Transmissibility of the Symbiotic Plasmid pRetCFN42d

Journal: Journal of Bacteriology

doi: 10.1128/JB.186.17.5753-5761.2004

Replicon localization of the Mob + DNA identified in cosmid pRe182R1a. Blots of EcoRI-digested genomic DNAs (A) and of intact plasmid profiles (Eckhardt gels) (B) hybridized against digoxigenin-labeled pRe182R1a as a probe are shown. Lanes: M, digoxigenin-labeled DNA molecular weight marker; 1, R. etli CE3 (wild type); 2, R. etli CFNX182(p42a − ); 3, R. etli CFNX183(p42b − ); 4, R. etli CFNX184(p42c − ); 5, R. etli CFNX89(p42d − ); 6 R. etli CFNX185(p42eΔ) ; 7, R. etli CFNX186(p42f − ); 8, R. etli CFNX218(p42a − , p42b − , p42c − , p42d − , p42eΔ, p42f − ).
Figure Legend Snippet: Replicon localization of the Mob + DNA identified in cosmid pRe182R1a. Blots of EcoRI-digested genomic DNAs (A) and of intact plasmid profiles (Eckhardt gels) (B) hybridized against digoxigenin-labeled pRe182R1a as a probe are shown. Lanes: M, digoxigenin-labeled DNA molecular weight marker; 1, R. etli CE3 (wild type); 2, R. etli CFNX182(p42a − ); 3, R. etli CFNX183(p42b − ); 4, R. etli CFNX184(p42c − ); 5, R. etli CFNX89(p42d − ); 6 R. etli CFNX185(p42eΔ) ; 7, R. etli CFNX186(p42f − ); 8, R. etli CFNX218(p42a − , p42b − , p42c − , p42d − , p42eΔ, p42f − ).

Techniques Used: Plasmid Preparation, Labeling, Molecular Weight, Marker

3) Product Images from "High-Throughput Microarray Detection of Vomeronasal Receptor Gene Expression in Rodents"

Article Title: High-Throughput Microarray Detection of Vomeronasal Receptor Gene Expression in Rodents

Journal: Frontiers in Neuroscience

doi: 10.3389/fnins.2010.00164

Temporal expression change of VR genes confirmed by in situ hybridization . One gene was selected from four main patterns shown in Figure 5 for in situ hybridization. The number of VR expressing vomeronasal sensory neurons at different developmental time points was counted with representative slides. In situ hybridization was performed in coronal sections of mouse VNO using digoxigenin-labeled antisense RNA probes. For each pattern from (A) to (D) , the overall time course expression patterns were shown, followed by two representative sections with positive label cells at two ages, then summarized the quantification of the positive labeled cells for each VR gene at each age. For each bar, three replicate mice were used. Section scale bar = 100 μm. (A,B) p > 0.1. (C,D) p
Figure Legend Snippet: Temporal expression change of VR genes confirmed by in situ hybridization . One gene was selected from four main patterns shown in Figure 5 for in situ hybridization. The number of VR expressing vomeronasal sensory neurons at different developmental time points was counted with representative slides. In situ hybridization was performed in coronal sections of mouse VNO using digoxigenin-labeled antisense RNA probes. For each pattern from (A) to (D) , the overall time course expression patterns were shown, followed by two representative sections with positive label cells at two ages, then summarized the quantification of the positive labeled cells for each VR gene at each age. For each bar, three replicate mice were used. Section scale bar = 100 μm. (A,B) p > 0.1. (C,D) p

Techniques Used: Expressing, In Situ Hybridization, Labeling, Mouse Assay

4) Product Images from "A novel GAA-repeat-expansion-based mouse model of Friedreich’s ataxia"

Article Title: A novel GAA-repeat-expansion-based mouse model of Friedreich’s ataxia

Journal: Disease Models & Mechanisms

doi: 10.1242/dmm.018952

Transgene copy number. (A) Two TaqMan copy-number assays were applied: Hs05092416-cn assay (ATX 416; represented in black) was designed to amplify a 106-bp fragment of FXN within intron 3, and Hs02407730-cn assay (ATX 730; represented in grey) was designed to amplify an 80-bp fragment of FXN within intron 1 and exon 2. Human mammary epithelial cell (HMEC) with copy numbers of two served as a calibrator. Error bars=s.d. n =2. (B) Determination of the integration site of the transgenic FXN gene by FISH. Biotin-labelled RP11-265B8 and digoxigenin-labelled RP11-876N18 probes were hybridised onto interphase and metaphase chromosomes (DAPI stained) of YG8sR cells. YG8sR showed one hybridisation signal, indicating a single integration site of the FXN transgene containing one copy of the FXN gene. Scale bars: 10 μm.
Figure Legend Snippet: Transgene copy number. (A) Two TaqMan copy-number assays were applied: Hs05092416-cn assay (ATX 416; represented in black) was designed to amplify a 106-bp fragment of FXN within intron 3, and Hs02407730-cn assay (ATX 730; represented in grey) was designed to amplify an 80-bp fragment of FXN within intron 1 and exon 2. Human mammary epithelial cell (HMEC) with copy numbers of two served as a calibrator. Error bars=s.d. n =2. (B) Determination of the integration site of the transgenic FXN gene by FISH. Biotin-labelled RP11-265B8 and digoxigenin-labelled RP11-876N18 probes were hybridised onto interphase and metaphase chromosomes (DAPI stained) of YG8sR cells. YG8sR showed one hybridisation signal, indicating a single integration site of the FXN transgene containing one copy of the FXN gene. Scale bars: 10 μm.

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

5) Product Images from "BMPER, a Novel Endothelial Cell Precursor-Derived Protein, Antagonizes Bone Morphogenetic Protein Signaling and Endothelial Cell Differentiation"

Article Title: BMPER, a Novel Endothelial Cell Precursor-Derived Protein, Antagonizes Bone Morphogenetic Protein Signaling and Endothelial Cell Differentiation

Journal: Molecular and Cellular Biology

doi: 10.1128/MCB.23.16.5664-5679.2003

Localization of BMPER mRNA in developing mouse embryos. (A) Whole-mount in situ hybridization of a mouse day 9.5 embryo with a digoxigenin-labeled BMPER antisense cDNA probe. Note the midline staining in the rostral telencephalon (arrow). Bar, 500 μm. (B) Transverse section from the same embryo at the level indicated in the diagram at the lower left. Bar, 80 μm. tv, telencephalic vesicle. (C) Magnification of the frontal area from panel B. Bar, 20 μm. (D) Transverse section of the embryo shown in panel A at the level indicated in the diagram. Bar, 80 μm. nt, neural tube; rp, Rathke's pouch; s, somite; nc, notochord. Cells that appear to be migrating ventrally toward the branchial arch and heart region express BMPER. (E to H) In situ hybridization of sections from a day 10.5 mouse embryo. Arrows indicate the AGM region. (E and F) Overview of BMPER staining (E) versus that of the sense control (F) at the level indicated in the diagram. Bar, 400 μm. (G) Magnification of panel E. Bar, 150 μm. da, dorsal aorta. Note the staining of cells ventrolateral to the dorsal aorta and a ring-shaped layer of stained cells around the dorsal aorta (arrowheads). (H) Magnification of panel F. Bar, 50 μm. pg, primitive gut.
Figure Legend Snippet: Localization of BMPER mRNA in developing mouse embryos. (A) Whole-mount in situ hybridization of a mouse day 9.5 embryo with a digoxigenin-labeled BMPER antisense cDNA probe. Note the midline staining in the rostral telencephalon (arrow). Bar, 500 μm. (B) Transverse section from the same embryo at the level indicated in the diagram at the lower left. Bar, 80 μm. tv, telencephalic vesicle. (C) Magnification of the frontal area from panel B. Bar, 20 μm. (D) Transverse section of the embryo shown in panel A at the level indicated in the diagram. Bar, 80 μm. nt, neural tube; rp, Rathke's pouch; s, somite; nc, notochord. Cells that appear to be migrating ventrally toward the branchial arch and heart region express BMPER. (E to H) In situ hybridization of sections from a day 10.5 mouse embryo. Arrows indicate the AGM region. (E and F) Overview of BMPER staining (E) versus that of the sense control (F) at the level indicated in the diagram. Bar, 400 μm. (G) Magnification of panel E. Bar, 150 μm. da, dorsal aorta. Note the staining of cells ventrolateral to the dorsal aorta and a ring-shaped layer of stained cells around the dorsal aorta (arrowheads). (H) Magnification of panel F. Bar, 50 μm. pg, primitive gut.

Techniques Used: In Situ Hybridization, Labeling, Staining

6) Product Images from "Novel simple sequence repeats (SSRs) detected by ND-FISH in heterochromatin of Drosophila melanogaster"

Article Title: Novel simple sequence repeats (SSRs) detected by ND-FISH in heterochromatin of Drosophila melanogaster

Journal: BMC Genomics

doi: 10.1186/1471-2164-12-205

Organization of representative SSRs in extended DNA fibres from neuroblast nuclei of D. melanogaster after ND-FISH with the indicated probes (green or red signals from digoxigenin- and biotin-labelled probes respectively) and DAPI (blue) staining . An example of two colour fibre ND-FISH in haloed nuclei with (AAGAC) 3 (red) and (AACAC) 3 (green) is shown in a . Examples of fluorescent signal patterns in fibres stretched to different degrees are shown in e (square insets). Note the characteristic beaded nature of the signals in the highly extended fibres. A representative of the gaps observed between the continuous track of beaded signals is amplified in f . Scale bar = 10 μm, except in f in which it represents 5 μm. Every micrometer represents 3 kb of the highly stretched DNA.
Figure Legend Snippet: Organization of representative SSRs in extended DNA fibres from neuroblast nuclei of D. melanogaster after ND-FISH with the indicated probes (green or red signals from digoxigenin- and biotin-labelled probes respectively) and DAPI (blue) staining . An example of two colour fibre ND-FISH in haloed nuclei with (AAGAC) 3 (red) and (AACAC) 3 (green) is shown in a . Examples of fluorescent signal patterns in fibres stretched to different degrees are shown in e (square insets). Note the characteristic beaded nature of the signals in the highly extended fibres. A representative of the gaps observed between the continuous track of beaded signals is amplified in f . Scale bar = 10 μm, except in f in which it represents 5 μm. Every micrometer represents 3 kb of the highly stretched DNA.

Techniques Used: Fluorescence In Situ Hybridization, Staining, Amplification

Chromosomal distribution of the mono- and dinucleotide SSRs in the salivary gland (a, d, e, and h) and neuroblast cells (b, c, f, i and j) of D. melanogaster after ND-FISH and DAPI staining . Both polytene chromosomes and diploid nuclei are shown in g; examples of two-colour ND-FISH with (AAGAG) 5 are shown in h (insets) and j . Each panel shows individual and/or merged images to facilitate the appreciation of the distribution of signals (green or red from digoxigenin- and biotin-labelled probes respectively) and identification of chromosomes. The localization of the signals with respect to the heterochromatic DAPI banding pattern in mitotic chromosomes is shown in Figure 4. Note the high concentration of A, C, AC and AG SSRs on polytene X chromosomes; this contrasts with the lesser presence of these repeats on chromosome 4. An enlarged view of the A repeat signals at the base of chromosome X (square) and chromosome 4 is shown at the right of panel a . The arrows point chromosomes 4; CR, chromocentre. Scale bar = 5 μm and 25 μm in (pro)metaphase and polytene nuclei respectively.
Figure Legend Snippet: Chromosomal distribution of the mono- and dinucleotide SSRs in the salivary gland (a, d, e, and h) and neuroblast cells (b, c, f, i and j) of D. melanogaster after ND-FISH and DAPI staining . Both polytene chromosomes and diploid nuclei are shown in g; examples of two-colour ND-FISH with (AAGAG) 5 are shown in h (insets) and j . Each panel shows individual and/or merged images to facilitate the appreciation of the distribution of signals (green or red from digoxigenin- and biotin-labelled probes respectively) and identification of chromosomes. The localization of the signals with respect to the heterochromatic DAPI banding pattern in mitotic chromosomes is shown in Figure 4. Note the high concentration of A, C, AC and AG SSRs on polytene X chromosomes; this contrasts with the lesser presence of these repeats on chromosome 4. An enlarged view of the A repeat signals at the base of chromosome X (square) and chromosome 4 is shown at the right of panel a . The arrows point chromosomes 4; CR, chromocentre. Scale bar = 5 μm and 25 μm in (pro)metaphase and polytene nuclei respectively.

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

Southern hybridization patterns of genomic DNA from female and male D. melanogaster digested by Alu I, Hinf I and Rsa I and fractionated by conventional 1% agarose gel electrophoresis ( A ) . Three filter transfers were sequentially hybridized with the indicated digoxigenin end-labelled SSR probes ( B to K ). Size markers (M) are given in kb.
Figure Legend Snippet: Southern hybridization patterns of genomic DNA from female and male D. melanogaster digested by Alu I, Hinf I and Rsa I and fractionated by conventional 1% agarose gel electrophoresis ( A ) . Three filter transfers were sequentially hybridized with the indicated digoxigenin end-labelled SSR probes ( B to K ). Size markers (M) are given in kb.

Techniques Used: Hybridization, Agarose Gel Electrophoresis

Photomicrographs showing the motif-dependent chromosomal distribution of the pentanucleotide probes in the salivary gland (a, c, f, g, i, m and n) and neuroblast cells (a, b, d, e, h, j, k, l, m and o) of male and female D. melanogaster after ND-FISH and DAPI staining . Each panel shows individual and/or merged images to facilitate the visualization of the signals (green or red for digoxigenin- and biotin-labelled probes respectively) with respect to the DAPI (blue) banding pattern. In some samples interphase and mitotic neuroblast nuclei are shown in the same panels; both polytene and diploid nuclei are shown in a and m . Mitotic chromosomes are identified as well as polytene regions of interest. An example of two-colour ND-FISH is shown in e . Note that only the diffuse chromocentre (CR) observed in polytene nuclei is enriched in pentanucleotide SSRs, which localize to specific heterochromatic regions in mitotic chromosomes as shown in Figure 4. The arrows point to low intensity signals. Scale bar: 5 μm, except in a and m , in which it represents 25 μm.
Figure Legend Snippet: Photomicrographs showing the motif-dependent chromosomal distribution of the pentanucleotide probes in the salivary gland (a, c, f, g, i, m and n) and neuroblast cells (a, b, d, e, h, j, k, l, m and o) of male and female D. melanogaster after ND-FISH and DAPI staining . Each panel shows individual and/or merged images to facilitate the visualization of the signals (green or red for digoxigenin- and biotin-labelled probes respectively) with respect to the DAPI (blue) banding pattern. In some samples interphase and mitotic neuroblast nuclei are shown in the same panels; both polytene and diploid nuclei are shown in a and m . Mitotic chromosomes are identified as well as polytene regions of interest. An example of two-colour ND-FISH is shown in e . Note that only the diffuse chromocentre (CR) observed in polytene nuclei is enriched in pentanucleotide SSRs, which localize to specific heterochromatic regions in mitotic chromosomes as shown in Figure 4. The arrows point to low intensity signals. Scale bar: 5 μm, except in a and m , in which it represents 25 μm.

Techniques Used: Fluorescence In Situ Hybridization, Staining

7) Product Images from "Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development"

Article Title: Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development

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

doi: 10.1073/pnas.0401389101

The mapping of C. intestinalis extended Hox genes onto metaphase chromosomes by using FISH. Metaphase chromosome spreads prepared from 64-cell stage embryos were hybridized with two or three probes labeled with digoxigenin (red) or biotin (green) for the genes indicated at the top in A – L . Red and green arrowheads indicate the signals for the gene of the same color code. In E and G , red arrowheads with a black dot indicate the signals for Ci-Hox2–4 .In A – E and G , enlargement of the chromosome with signals is indicated in Insets . (Bars, 5 μm.)
Figure Legend Snippet: The mapping of C. intestinalis extended Hox genes onto metaphase chromosomes by using FISH. Metaphase chromosome spreads prepared from 64-cell stage embryos were hybridized with two or three probes labeled with digoxigenin (red) or biotin (green) for the genes indicated at the top in A – L . Red and green arrowheads indicate the signals for the gene of the same color code. In E and G , red arrowheads with a black dot indicate the signals for Ci-Hox2–4 .In A – E and G , enlargement of the chromosome with signals is indicated in Insets . (Bars, 5 μm.)

Techniques Used: Fluorescence In Situ Hybridization, Labeling

8) Product Images from "A novel FISH technique for labeling the chromosomes of dinoflagellates in suspension"

Article Title: A novel FISH technique for labeling the chromosomes of dinoflagellates in suspension

Journal: PLoS ONE

doi: 10.1371/journal.pone.0204382

FISH mapping of different repeat sequences in nuclei isolated using the chromosome isolation procedure. (A) K . brevis and (B, C) K . mikimotoi . DAPI-stained DNA (blue) and in situ hybridization of the 45S rDNA digoxigenin-labeled probe (green) in combination with (A) the Dy547-labeled telomeric probe (red) or (C) the biotin-labeled (AG) 10 probe (red). Note the largely disturbed nuclear morphology after FISH. Scale bar = 10 μm.
Figure Legend Snippet: FISH mapping of different repeat sequences in nuclei isolated using the chromosome isolation procedure. (A) K . brevis and (B, C) K . mikimotoi . DAPI-stained DNA (blue) and in situ hybridization of the 45S rDNA digoxigenin-labeled probe (green) in combination with (A) the Dy547-labeled telomeric probe (red) or (C) the biotin-labeled (AG) 10 probe (red). Note the largely disturbed nuclear morphology after FISH. Scale bar = 10 μm.

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

9) Product Images from "Asymmetric bidirectional replication at the human DBF4 origin"

Article Title: Asymmetric bidirectional replication at the human DBF4 origin

Journal:

doi: 10.1038/nsmb.1439

Determining RIPs at the DBF4 locus in asynchronous HeLa cells. ( a ) Primer extension with the indicated digoxigenin-labeled primers (pA, pB and pC) using nascent DNA (1–2 kb) isolated from asynchronous HeLa cells that had been incubated for 1 h
Figure Legend Snippet: Determining RIPs at the DBF4 locus in asynchronous HeLa cells. ( a ) Primer extension with the indicated digoxigenin-labeled primers (pA, pB and pC) using nascent DNA (1–2 kb) isolated from asynchronous HeLa cells that had been incubated for 1 h

Techniques Used: Labeling, Isolation, Incubation

10) Product Images from "Glycoproteins gM and gN of Pseudorabies Virus Are Dispensable for Viral Penetration and Propagation in the Nervous Systems of Adult Mice"

Article Title: Glycoproteins gM and gN of Pseudorabies Virus Are Dispensable for Viral Penetration and Propagation in the Nervous Systems of Adult Mice

Journal: Journal of Virology

doi:

Genotype assessment of the viral stocks. (A) Southern analysis of wild-type (WT) PrV, gM − and gN − mutants, and revertants. After extraction, viral DNA was digested with either Bam HI (WT, gM − , and gM R ) or Pst I (gN R , gN − , and WT). Fragments were separated on a 0.6% agarose gel containing ethidium bromide (gel a), transferred to a nylon membrane, and hybridized with a LacZ probe (pGEM 3Zf; Promega) labeled with digoxigenin (gel b). Size markers (M) are on the left. (B) PCR amplifications were done with around 20 ng of wild-type or mutant DNA, 1 pmol of each primer, 2.5 U of Taq DNA polymerase (Appligene), 50 μM concentration of each deoxynucleoside triphosphate, and 10% dimethyl sulfoxide per reaction mixture. In addition to mutant DNA, 2, 20, and 200 pg of wild-type PrV DNA were added to samples 6 and 11, 7 and 12, and 8 and 13, respectively. Thirty cycles of amplification at 95, 50, and 72°C for 60, 40, and 120 s, respectively, were performed. PCR products were separated in 2% agarose gels containing ethidium bromide and were visualized in UV light. A pBR322 DNA- Msp I digest was used for size markers (sizes of the bands, 217, 238, 242, and 307 nucleotides). Numbers at the left are molecular sizes of the amplified products, in nucleotides.
Figure Legend Snippet: Genotype assessment of the viral stocks. (A) Southern analysis of wild-type (WT) PrV, gM − and gN − mutants, and revertants. After extraction, viral DNA was digested with either Bam HI (WT, gM − , and gM R ) or Pst I (gN R , gN − , and WT). Fragments were separated on a 0.6% agarose gel containing ethidium bromide (gel a), transferred to a nylon membrane, and hybridized with a LacZ probe (pGEM 3Zf; Promega) labeled with digoxigenin (gel b). Size markers (M) are on the left. (B) PCR amplifications were done with around 20 ng of wild-type or mutant DNA, 1 pmol of each primer, 2.5 U of Taq DNA polymerase (Appligene), 50 μM concentration of each deoxynucleoside triphosphate, and 10% dimethyl sulfoxide per reaction mixture. In addition to mutant DNA, 2, 20, and 200 pg of wild-type PrV DNA were added to samples 6 and 11, 7 and 12, and 8 and 13, respectively. Thirty cycles of amplification at 95, 50, and 72°C for 60, 40, and 120 s, respectively, were performed. PCR products were separated in 2% agarose gels containing ethidium bromide and were visualized in UV light. A pBR322 DNA- Msp I digest was used for size markers (sizes of the bands, 217, 238, 242, and 307 nucleotides). Numbers at the left are molecular sizes of the amplified products, in nucleotides.

Techniques Used: Agarose Gel Electrophoresis, Labeling, Polymerase Chain Reaction, Mutagenesis, Concentration Assay, Amplification

11) Product Images from "Multiple kinesins induce tension for smooth cargo transport"

Article Title: Multiple kinesins induce tension for smooth cargo transport

Journal: eLife

doi: 10.7554/eLife.50974

Forced detachment traces and velocities. ( a ) Nine pulling traces right before forced detachment of kinesin-QD, rupturing supposedly the weakest link in the coverslip-DNA-QD-kinesin interaction, which is the digoxigenin:anti-digoxigenin interaction. ( b ) The velocities of the last five frames before the forced detachment for all nine traces. The velocities (of kinesin relative to the glass coverslip) vary from 7 nm/s to 427 nm/s.
Figure Legend Snippet: Forced detachment traces and velocities. ( a ) Nine pulling traces right before forced detachment of kinesin-QD, rupturing supposedly the weakest link in the coverslip-DNA-QD-kinesin interaction, which is the digoxigenin:anti-digoxigenin interaction. ( b ) The velocities of the last five frames before the forced detachment for all nine traces. The velocities (of kinesin relative to the glass coverslip) vary from 7 nm/s to 427 nm/s.

Techniques Used:

Dual optical trap assay to measure the rupture force for digoxigenin:anti-digoxigenin interaction. Two polystyrene beads are bound to the opposite ends of 1,565 bp DNA through biotin-streptavidin linkage and digoxigenin:anti-digoxigenin linkage, which is the weaker of the two. The beads are captured in optical traps and are pulled away from one another until the digoxigenin:anti-digoxigenin linkage ruptures.
Figure Legend Snippet: Dual optical trap assay to measure the rupture force for digoxigenin:anti-digoxigenin interaction. Two polystyrene beads are bound to the opposite ends of 1,565 bp DNA through biotin-streptavidin linkage and digoxigenin:anti-digoxigenin linkage, which is the weaker of the two. The beads are captured in optical traps and are pulled away from one another until the digoxigenin:anti-digoxigenin linkage ruptures.

Techniques Used: TRAP Assay

12) Product Images from "Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics"

Article Title: Analysis of proteomic profiles and functional properties of human peripheral blood myeloid dendritic cells, monocyte-derived dendritic cells and the dendritic cell-like KG-1 cells reveals distinct characteristics

Journal: Genome Biology

doi: 10.1186/gb-2007-8-3-r30

ELISA detection of cell lysate proteins. Differentially expressed digoxigenin-labeled proteins of mDCs, moDCs and KG-1 cell lysates were captured by specific antibody coated plates and detected with a polyclonal anti-dioxigenin Fab fragment. Data are representative of two experiments.
Figure Legend Snippet: ELISA detection of cell lysate proteins. Differentially expressed digoxigenin-labeled proteins of mDCs, moDCs and KG-1 cell lysates were captured by specific antibody coated plates and detected with a polyclonal anti-dioxigenin Fab fragment. Data are representative of two experiments.

Techniques Used: Enzyme-linked Immunosorbent Assay, Labeling

13) Product Images from "Deletion of human metapneumovirus M2-2 increases mutation frequency and attenuates growth in hamsters"

Article Title: Deletion of human metapneumovirus M2-2 increases mutation frequency and attenuates growth in hamsters

Journal: Virology Journal

doi: 10.1186/1743-422X-5-69

4-day time course of Northern blot analysis and multicycle growth . Replicate cultures of Vero cells were infected with rhMPV or rhMPV/ΔM2-2 at MOI of 0.1 PFU/cell. Cells and supernatants were harvested daily. Total RNA was extracted, and 7 replicate aliquots were separated on 1% agarose gel in the presence of 0.44 M formaldehyde gel, transferred to a nylon membrane and hybridized with digoxigenin-labeled single-stranded anti-sense riboprobes to detect mRNA as follows: A) M2 riboprobe; B) SH riboprobe; C) N riboprobe; D) F riboprobe; E) G riboprobe. F) Sense P, M, and F riboprobes were combined to detect genomic RNA. G) RNA in a duplicate gel was visualized with ethidium bromide and photographed under UV light. H) Titers of samples prior to RNA extraction were determined by plaque assay in Vero cells.
Figure Legend Snippet: 4-day time course of Northern blot analysis and multicycle growth . Replicate cultures of Vero cells were infected with rhMPV or rhMPV/ΔM2-2 at MOI of 0.1 PFU/cell. Cells and supernatants were harvested daily. Total RNA was extracted, and 7 replicate aliquots were separated on 1% agarose gel in the presence of 0.44 M formaldehyde gel, transferred to a nylon membrane and hybridized with digoxigenin-labeled single-stranded anti-sense riboprobes to detect mRNA as follows: A) M2 riboprobe; B) SH riboprobe; C) N riboprobe; D) F riboprobe; E) G riboprobe. F) Sense P, M, and F riboprobes were combined to detect genomic RNA. G) RNA in a duplicate gel was visualized with ethidium bromide and photographed under UV light. H) Titers of samples prior to RNA extraction were determined by plaque assay in Vero cells.

Techniques Used: Northern Blot, Infection, Agarose Gel Electrophoresis, Labeling, RNA Extraction, Plaque Assay

14) Product Images from "Human lung cancer cells express functionally active Toll-like receptor 9"

Article Title: Human lung cancer cells express functionally active Toll-like receptor 9

Journal: Respiratory Research

doi: 10.1186/1465-9921-6-1

Immunohistochemistry (IHC) (A-C) for TLR9 detected by a mouse monoclonal antibody. Adenocarcinoma of the lung (A) . Squamous cell carcinoma of the lung (B) . A549 cells (all 600 ×) (C) . In situ hybridization (ISH) targeting mRNA of human TLR9 with a digoxigenin-labeled DNA-probe in a squamous cell carcinoma of the lung (600 ×) (D) . Immunohistochemical staining of TLR9-expression-levels in nonmalignant (E) and malignant tissues (F) derived from the same lungs an stained by the use of tissue arrays. Results of RT-PCR targeting TLR9 in cell lines (G) . M: molecular-weight marker (MW8, Roche). 1: negative control; 2: A549; 3: NCI-H727; 4: BEAS 2b; 5: Mononuclear cells from a healthy human donor. Confocal laser microscopy of A549 cells transiently transfected with a GFP-TLR9 plasmid: Cytoplasmic expression of TLR9 is observable in all cells, while successful transfection led to overexpression of TLR9 resulting in bright GFP signals completely superimposed by the TLR9 antibody signal (H) . Nuclear counterstain was performed with TOTO3.
Figure Legend Snippet: Immunohistochemistry (IHC) (A-C) for TLR9 detected by a mouse monoclonal antibody. Adenocarcinoma of the lung (A) . Squamous cell carcinoma of the lung (B) . A549 cells (all 600 ×) (C) . In situ hybridization (ISH) targeting mRNA of human TLR9 with a digoxigenin-labeled DNA-probe in a squamous cell carcinoma of the lung (600 ×) (D) . Immunohistochemical staining of TLR9-expression-levels in nonmalignant (E) and malignant tissues (F) derived from the same lungs an stained by the use of tissue arrays. Results of RT-PCR targeting TLR9 in cell lines (G) . M: molecular-weight marker (MW8, Roche). 1: negative control; 2: A549; 3: NCI-H727; 4: BEAS 2b; 5: Mononuclear cells from a healthy human donor. Confocal laser microscopy of A549 cells transiently transfected with a GFP-TLR9 plasmid: Cytoplasmic expression of TLR9 is observable in all cells, while successful transfection led to overexpression of TLR9 resulting in bright GFP signals completely superimposed by the TLR9 antibody signal (H) . Nuclear counterstain was performed with TOTO3.

Techniques Used: Immunohistochemistry, In Situ Hybridization, Labeling, Staining, Expressing, Derivative Assay, Reverse Transcription Polymerase Chain Reaction, Molecular Weight, Marker, Negative Control, Microscopy, Transfection, Plasmid Preparation, Over Expression

15) Product Images from "MicroRNA-like viral small RNA from porcine reproductive and respiratory syndrome virus negatively regulates viral replication by targeting the viral nonstructural protein 2"

Article Title: MicroRNA-like viral small RNA from porcine reproductive and respiratory syndrome virus negatively regulates viral replication by targeting the viral nonstructural protein 2

Journal: Oncotarget

doi: 10.18632/oncotarget.12703

Prediction and identification of PRRSV-encoded miRNA A. Schematic diagram of predicted miRNAs in the PRRSV (GD-HD strain) viral genome RNA. B. Secondary structure of precursors to PRRSV-vsRNA1-4. C. PRRSV-vsRNA1 (black arrow) in mock- or PRRSV-infected PAM cells were detected with digoxigenin-labeled probes containing oligonucleotides complementary to PRRSV-vsRNA1. The 28S and 18S RNA bands stained with ethidium bromide are displayed to demonstrate equal loading. D. Cloning validation of the predicted PRRSV-vsRNA1 in PRRSV-infected PAM cells. Sequencing results for the PRRSV-vsRNA1 and primer sequences are underlined in the sequence maps.
Figure Legend Snippet: Prediction and identification of PRRSV-encoded miRNA A. Schematic diagram of predicted miRNAs in the PRRSV (GD-HD strain) viral genome RNA. B. Secondary structure of precursors to PRRSV-vsRNA1-4. C. PRRSV-vsRNA1 (black arrow) in mock- or PRRSV-infected PAM cells were detected with digoxigenin-labeled probes containing oligonucleotides complementary to PRRSV-vsRNA1. The 28S and 18S RNA bands stained with ethidium bromide are displayed to demonstrate equal loading. D. Cloning validation of the predicted PRRSV-vsRNA1 in PRRSV-infected PAM cells. Sequencing results for the PRRSV-vsRNA1 and primer sequences are underlined in the sequence maps.

Techniques Used: Infection, Labeling, Staining, Clone Assay, Sequencing

16) Product Images from "A Novel Mechanism of Growth Phase-dependent Tolerance to Isoniazid in Mycobacteria *"

Article Title: A Novel Mechanism of Growth Phase-dependent Tolerance to Isoniazid in Mycobacteria *

Journal: The Journal of Biological Chemistry

doi: 10.1074/jbc.M111.333385

Gel-shift assay to analyze the interaction between MDP1 and the furA-katG DNA promoter region. Recombinant MDP1 was incubated with either digoxigenin ( DIG )-labeled DNA probes including the sequence of the furA-katG promoter region alone, or together with
Figure Legend Snippet: Gel-shift assay to analyze the interaction between MDP1 and the furA-katG DNA promoter region. Recombinant MDP1 was incubated with either digoxigenin ( DIG )-labeled DNA probes including the sequence of the furA-katG promoter region alone, or together with

Techniques Used: Electrophoretic Mobility Shift Assay, Recombinant, Incubation, Labeling, Sequencing

17) Product Images from "Mutually Exclusive Glomerular Innervation by Two Distinct Types of Olfactory Sensory Neurons Revealed in Transgenic Zebrafish"

Article Title: Mutually Exclusive Glomerular Innervation by Two Distinct Types of Olfactory Sensory Neurons Revealed in Transgenic Zebrafish

Journal: The Journal of Neuroscience

doi: 10.1523/JNEUROSCI.0679-05.2005

Two distinct types of OSNs with different molecular signatures in zebrafish OE. A-J , RNA in situ hybridization was performed on horizontal sections of the zebrafish olfactory rosette using digoxigenin-labeled probes specific for the following molecules: zOMP ( A , B ), zCNGA2 ( C ), zOR2.1 ( D ), zOR13.1 ( E ), zTRPC2 ( F , G ), zVR5.3 ( H ), zVR3.13a ( I ), and zVR3.13b ( J ). Note that zOMP ( B ), zCNGA2 ( C ), and OR -type receptors ( D , E ) were expressed in the deep layer of the OE, whereas zTRPC2 ( G ) and VR -type receptors ( H-J ) were expressed in the superficial layer. In contrast to the zVR5.3 expression in a large fraction of OSNs ( H ), other VR - and OR -type receptors were expressed in a small subset of OSNs ( D , E , I , J ). B-E , G-J , The apical surface of the OE is at the top of each panel. Scale bars: (in F ) A , F , 100 μm; (in J ) B-E , G-J , 20 μm.
Figure Legend Snippet: Two distinct types of OSNs with different molecular signatures in zebrafish OE. A-J , RNA in situ hybridization was performed on horizontal sections of the zebrafish olfactory rosette using digoxigenin-labeled probes specific for the following molecules: zOMP ( A , B ), zCNGA2 ( C ), zOR2.1 ( D ), zOR13.1 ( E ), zTRPC2 ( F , G ), zVR5.3 ( H ), zVR3.13a ( I ), and zVR3.13b ( J ). Note that zOMP ( B ), zCNGA2 ( C ), and OR -type receptors ( D , E ) were expressed in the deep layer of the OE, whereas zTRPC2 ( G ) and VR -type receptors ( H-J ) were expressed in the superficial layer. In contrast to the zVR5.3 expression in a large fraction of OSNs ( H ), other VR - and OR -type receptors were expressed in a small subset of OSNs ( D , E , I , J ). B-E , G-J , The apical surface of the OE is at the top of each panel. Scale bars: (in F ) A , F , 100 μm; (in J ) B-E , G-J , 20 μm.

Techniques Used: RNA In Situ Hybridization, Labeling, Expressing

18) Product Images from "Biofortified indica rice attains iron and zinc nutrition dietary targets in the field"

Article Title: Biofortified indica rice attains iron and zinc nutrition dietary targets in the field

Journal: Scientific Reports

doi: 10.1038/srep19792

Strategy for the development of biofortified high-iron rice and the Fe concentration achieved in T 2 polished seeds. ( a ) Schematic diagram of the T-DNA constructs prepared for rice transformation for the purposes of our study. RB and LB represent the right and left borders of the T-DNA, respectively; pr1: represents the constitutive promoters pr35S with single enhancer (pr35Sse), maize ubiquitin promoter, or rice endosperm-specific promoter glutelinB1; pr2: represents the rice endosperm-specific promoters glutelinB1 or glutelinA2; pr35Sde represents the constitutive promoter pr35S with double enhancer; OsNAS2 : Oryza sativa nicotianamine synthase 2; SferH-1 : Glycine max ferritin subunit H-1; hpt : hygromycin phosphotransferase; 3′nos: 3′UTR of nopaline synthase; 3′35S: 3′UTR of 35S cauliflower mosaic virus gene. The horizontal line below SferH-1 represents the deduced hybridization position of the digoxigenin-labeled cDNA probe; E: Eco RI. ( b ) Flow-chart displaying the steps that have been followed for the development of biofortified high-Fe/-Zn rice. ( c ) Fe concentration (μg g −1 DW) of polished seeds harvested from T 1 homozygous plants of representative NAS, Fer, and NASFer events, null segregant, and non-transformed rice under screenhouse conditions. Bars represent the means ± s.d. of three replicates.
Figure Legend Snippet: Strategy for the development of biofortified high-iron rice and the Fe concentration achieved in T 2 polished seeds. ( a ) Schematic diagram of the T-DNA constructs prepared for rice transformation for the purposes of our study. RB and LB represent the right and left borders of the T-DNA, respectively; pr1: represents the constitutive promoters pr35S with single enhancer (pr35Sse), maize ubiquitin promoter, or rice endosperm-specific promoter glutelinB1; pr2: represents the rice endosperm-specific promoters glutelinB1 or glutelinA2; pr35Sde represents the constitutive promoter pr35S with double enhancer; OsNAS2 : Oryza sativa nicotianamine synthase 2; SferH-1 : Glycine max ferritin subunit H-1; hpt : hygromycin phosphotransferase; 3′nos: 3′UTR of nopaline synthase; 3′35S: 3′UTR of 35S cauliflower mosaic virus gene. The horizontal line below SferH-1 represents the deduced hybridization position of the digoxigenin-labeled cDNA probe; E: Eco RI. ( b ) Flow-chart displaying the steps that have been followed for the development of biofortified high-Fe/-Zn rice. ( c ) Fe concentration (μg g −1 DW) of polished seeds harvested from T 1 homozygous plants of representative NAS, Fer, and NASFer events, null segregant, and non-transformed rice under screenhouse conditions. Bars represent the means ± s.d. of three replicates.

Techniques Used: Concentration Assay, Construct, Transformation Assay, Hybridization, Labeling, Flow Cytometry

19) Product Images from "Oligonucleotide Array for Identification and Detection of Pythium Species †"

Article Title: Oligonucleotide Array for Identification and Detection of Pythium Species †

Journal:

doi: 10.1128/AEM.72.4.2691-2706.2006

Chemiluminograms showing hybridization patterns of digoxigenin-labeled amplicons obtained after PCR amplification of DNAs of pure cultures of P. aristosporium (A) and P. grandisporangium (B). Amino-linked oligonucleotides were spotted in duplicate, hybridized
Figure Legend Snippet: Chemiluminograms showing hybridization patterns of digoxigenin-labeled amplicons obtained after PCR amplification of DNAs of pure cultures of P. aristosporium (A) and P. grandisporangium (B). Amino-linked oligonucleotides were spotted in duplicate, hybridized

Techniques Used: Hybridization, Labeling, Polymerase Chain Reaction, Amplification

Summary of hybridization patterns of digoxigenin-labeled PCR amplicons of Pythium species to an array of species- and group-specific oligonucleotides on nylon membranes. Chemiluminograms were scanned on a 16-bit gray scale with Fotolook Ps 2.08 software
Figure Legend Snippet: Summary of hybridization patterns of digoxigenin-labeled PCR amplicons of Pythium species to an array of species- and group-specific oligonucleotides on nylon membranes. Chemiluminograms were scanned on a 16-bit gray scale with Fotolook Ps 2.08 software

Techniques Used: Hybridization, Labeling, Polymerase Chain Reaction, Software

Hybridization patterns of digoxigenin-labeled PCR amplicons obtained by direct processing of soil. One representative sample out of four replicates that had very similar hybridization patterns and showed the same species complex. Spots A1 to A5 are universal,
Figure Legend Snippet: Hybridization patterns of digoxigenin-labeled PCR amplicons obtained by direct processing of soil. One representative sample out of four replicates that had very similar hybridization patterns and showed the same species complex. Spots A1 to A5 are universal,

Techniques Used: Hybridization, Labeling, Polymerase Chain Reaction

20) Product Images from "Characterization of the Pasteurella multocida hgbA Gene Encoding a Hemoglobin-Binding Protein "

Article Title: Characterization of the Pasteurella multocida hgbA Gene Encoding a Hemoglobin-Binding Protein

Journal: Infection and Immunity

doi: 10.1128/IAI.70.11.5955-5964.2002

Presence of the hgbA gene in P. multocida strains: dot blot hybridization of chromosomal DNA from 34 P. multocida strains obtained from different animal sources and belonging to several serotypes with a digoxigenin-labeled 989-bp internal fragment of the hgbA gene. The DNA position corresponding to each of the strains is indicated above the nitrocellulose membrane. Equal amounts of chromosomal DNA (1 μg) of all strains were applied to the nitrocellulose membrane, and hybridization was performed under high-stringency conditions.
Figure Legend Snippet: Presence of the hgbA gene in P. multocida strains: dot blot hybridization of chromosomal DNA from 34 P. multocida strains obtained from different animal sources and belonging to several serotypes with a digoxigenin-labeled 989-bp internal fragment of the hgbA gene. The DNA position corresponding to each of the strains is indicated above the nitrocellulose membrane. Equal amounts of chromosomal DNA (1 μg) of all strains were applied to the nitrocellulose membrane, and hybridization was performed under high-stringency conditions.

Techniques Used: Dot Blot, Hybridization, Labeling

21) Product Images from "Cellular, Molecular and Functional Characterisation of YAC Transgenic Mouse Models of Friedreich Ataxia"

Article Title: Cellular, Molecular and Functional Characterisation of YAC Transgenic Mouse Models of Friedreich Ataxia

Journal: PLoS ONE

doi: 10.1371/journal.pone.0107416

Transgene copy number. ( a ) Two TaqMan copy number assays were applied; Hs05092416-cn assay, represented in black, was designed to amplify a 106 bp fragment of FXN within intron 3 and Hs02407730-cn assay, represented in grey, was designed to amplify an 80 bp fragment of FXN within intron 1 and exon 2. Wild type (WT) served as a negative control with no copy number. Error bars = SD. n = 2. ( b and c ) Determination of the integration site of the transgenic FXN gene by FISH. Biotin-labelled RP11-265B8 and digoxigenin- labelled RP11-876N18 probes were hybridised onto interphase and metaphase chromosomes (DAPI stained) of YG8R, YG22R and Y47R cells. ( b ) All three cell lines showed a single integration site of the FXN transgene by metaphase analysis. ( c ) YG8R showed three hybridisation signals corresponded to the transgenic FXN , whereas YG22R and Y47R showed one signal indicating one copy of the FXN transgene. Scale bare = 10 µm.
Figure Legend Snippet: Transgene copy number. ( a ) Two TaqMan copy number assays were applied; Hs05092416-cn assay, represented in black, was designed to amplify a 106 bp fragment of FXN within intron 3 and Hs02407730-cn assay, represented in grey, was designed to amplify an 80 bp fragment of FXN within intron 1 and exon 2. Wild type (WT) served as a negative control with no copy number. Error bars = SD. n = 2. ( b and c ) Determination of the integration site of the transgenic FXN gene by FISH. Biotin-labelled RP11-265B8 and digoxigenin- labelled RP11-876N18 probes were hybridised onto interphase and metaphase chromosomes (DAPI stained) of YG8R, YG22R and Y47R cells. ( b ) All three cell lines showed a single integration site of the FXN transgene by metaphase analysis. ( c ) YG8R showed three hybridisation signals corresponded to the transgenic FXN , whereas YG22R and Y47R showed one signal indicating one copy of the FXN transgene. Scale bare = 10 µm.

Techniques Used: Negative Control, Transgenic Assay, Fluorescence In Situ Hybridization, Staining, Hybridization

22) Product Images from "The Insulin Receptor in Astrocytes is Involved in the Entrance of Circulating Insulin into the Brain"

Article Title: The Insulin Receptor in Astrocytes is Involved in the Entrance of Circulating Insulin into the Brain

Journal: bioRxiv

doi: 10.1101/720813

Insulin receptors in astrocytes are required for neurons to capture circulating insulin. A , Intra-carotid injection of digoxigenin-labeled insulin (Diginsulin) results in its neuronal accumulation only when astrocytes express IR (no tamoxifen). Panel a shows astrocyte end-feet (GFAP + in green) ensheathing brain capillaries in control (-tamoxifen) mice receiving Dig-insulin injections. No Dig staining is seen. In contrast, Dig staining is seen in cell of panel b (white dotted square) with neuronal morphology (red), that are magnified in panel c (white asterisks). B , Accumulation of labeled insulin is readily seen in hippocampal neurons (NeuN + cells) of control mice (no tamoxifen). C , GFAP IR KO mice (treated with tamoxifen) do not show Dig staining in neurons after intracarotid injection of Dig-insulin. In panel a, vessels surrounded by GFAP + astroglial end-feet show abundant digoxigenin staining, suggesting lower transfer of Dig-insulin into the brain. In panels b and c (higher magnification of dotted white square in b) neuronal-like shapes with Dig staining are absent. Note the pronounced GFAP reactivity of astrocytes as compared to panel c in A. D , GFAP IR KO (+tamoxifen) do not show NeuN + (green) cells co-labelled with Dig in the hippocampal granular cell layer. Green: GFAP + or NeuN + cells; Red: Digoxigenin + cells.
Figure Legend Snippet: Insulin receptors in astrocytes are required for neurons to capture circulating insulin. A , Intra-carotid injection of digoxigenin-labeled insulin (Diginsulin) results in its neuronal accumulation only when astrocytes express IR (no tamoxifen). Panel a shows astrocyte end-feet (GFAP + in green) ensheathing brain capillaries in control (-tamoxifen) mice receiving Dig-insulin injections. No Dig staining is seen. In contrast, Dig staining is seen in cell of panel b (white dotted square) with neuronal morphology (red), that are magnified in panel c (white asterisks). B , Accumulation of labeled insulin is readily seen in hippocampal neurons (NeuN + cells) of control mice (no tamoxifen). C , GFAP IR KO mice (treated with tamoxifen) do not show Dig staining in neurons after intracarotid injection of Dig-insulin. In panel a, vessels surrounded by GFAP + astroglial end-feet show abundant digoxigenin staining, suggesting lower transfer of Dig-insulin into the brain. In panels b and c (higher magnification of dotted white square in b) neuronal-like shapes with Dig staining are absent. Note the pronounced GFAP reactivity of astrocytes as compared to panel c in A. D , GFAP IR KO (+tamoxifen) do not show NeuN + (green) cells co-labelled with Dig in the hippocampal granular cell layer. Green: GFAP + or NeuN + cells; Red: Digoxigenin + cells.

Techniques Used: Injection, Labeling, Mouse Assay, Staining

23) Product Images from "Generation and Characterization of Rac3 Knockout Mice"

Article Title: Generation and Characterization of Rac3 Knockout Mice

Journal: Molecular and Cellular Biology

doi: 10.1128/MCB.25.13.5763-5776.2005

Expression of Rac3 mRNA in E13 mice. Parasagittal sections of E12.5 to E13 wild-type (wt) and knockout (ko) mouse embryos were hybridized with antisense (AS) or sense (S) digoxigenin-labeled cRNAs for Rac3 and examined for signal detection. (A) Rac3 is specifically and widely expressed in the developing nervous system. (B) Cerebellum; (C) mesencephalon; (D and E) medulla oblongata; (F) trigeminal ganglion; (G) eye; (H and I) dorsal root ganglia; (J and K) spinal cord. Abbreviations: ctz, cortical transitory zone; dcn, deep cerebellar nuclei; di, diencephalon; drg, dorsal root ganglia; hb, hindbrain; he, heart; li, liver; lu, lung; mc, mouth cavity; me, mesencephalon; mg, midgut; nc, nasal cavity; ob, olfactory bulb; re, rectum; sc, spinal cord; se, septum; te, telencephalic vesicle. Bars: 500 μm (A); 200 μm (B to K).
Figure Legend Snippet: Expression of Rac3 mRNA in E13 mice. Parasagittal sections of E12.5 to E13 wild-type (wt) and knockout (ko) mouse embryos were hybridized with antisense (AS) or sense (S) digoxigenin-labeled cRNAs for Rac3 and examined for signal detection. (A) Rac3 is specifically and widely expressed in the developing nervous system. (B) Cerebellum; (C) mesencephalon; (D and E) medulla oblongata; (F) trigeminal ganglion; (G) eye; (H and I) dorsal root ganglia; (J and K) spinal cord. Abbreviations: ctz, cortical transitory zone; dcn, deep cerebellar nuclei; di, diencephalon; drg, dorsal root ganglia; hb, hindbrain; he, heart; li, liver; lu, lung; mc, mouth cavity; me, mesencephalon; mg, midgut; nc, nasal cavity; ob, olfactory bulb; re, rectum; sc, spinal cord; se, septum; te, telencephalic vesicle. Bars: 500 μm (A); 200 μm (B to K).

Techniques Used: Expressing, Mouse Assay, Knock-Out, Labeling

24) Product Images from "Opposing Roles of Double-Stranded RNA Effector Pathways and Viral Defense Proteins Revealed with CRISPR-Cas9 Knockout Cell Lines and Vaccinia Virus Mutants"

Article Title: Opposing Roles of Double-Stranded RNA Effector Pathways and Viral Defense Proteins Revealed with CRISPR-Cas9 Knockout Cell Lines and Vaccinia Virus Mutants

Journal: Journal of Virology

doi: 10.1128/JVI.00869-16

Viral gene expression in HAP1 KO cells. (A to D) Western blotting. Control, RNase L KO, PKR KO, and DKO HAP1 cells were infected with 5 PFU/cell of purified vD10rev, vD9muD10mu, or vΔE3L and harvested at the indicated times (shown in hours). The lysates were analyzed by Western blotting using antibodies to VACV (A), the E3 early protein (B), the D13 intermediate protein (C), and the A3 late protein (D). Antibody to actin served as a loading control (not shown). One set of cells was infected in the presence of AraC to inhibit viral DNA replication and confirm the stage of expression of the viral proteins. (E) Northern blotting. HAP1 control, RNase L KO, PKR KO, and DKO cells were mock infected or infected with 5 PFU/cell of purified vD10rev, vD9muD10mu, or vΔE3L virus. At 13 h after infection, the cells were harvested, and the total RNAs were isolated and resolved on glyoxal gels. rRNAs were stained with ethidium bromide and detected by UV fluorescence; reverse images are shown. The RNAs were transferred to a nylon membrane, incubated with the digoxigenin-labeled probes to the viral early C11 mRNA, viral late F17 mRNA, and cellular GAPDH mRNA, detected with alkaline phosphatase-conjugated antibody to digoxigenin, and visualized with the chemiluminescence substrate and X-ray film. p.i., postinfection; Ab, antibody.
Figure Legend Snippet: Viral gene expression in HAP1 KO cells. (A to D) Western blotting. Control, RNase L KO, PKR KO, and DKO HAP1 cells were infected with 5 PFU/cell of purified vD10rev, vD9muD10mu, or vΔE3L and harvested at the indicated times (shown in hours). The lysates were analyzed by Western blotting using antibodies to VACV (A), the E3 early protein (B), the D13 intermediate protein (C), and the A3 late protein (D). Antibody to actin served as a loading control (not shown). One set of cells was infected in the presence of AraC to inhibit viral DNA replication and confirm the stage of expression of the viral proteins. (E) Northern blotting. HAP1 control, RNase L KO, PKR KO, and DKO cells were mock infected or infected with 5 PFU/cell of purified vD10rev, vD9muD10mu, or vΔE3L virus. At 13 h after infection, the cells were harvested, and the total RNAs were isolated and resolved on glyoxal gels. rRNAs were stained with ethidium bromide and detected by UV fluorescence; reverse images are shown. The RNAs were transferred to a nylon membrane, incubated with the digoxigenin-labeled probes to the viral early C11 mRNA, viral late F17 mRNA, and cellular GAPDH mRNA, detected with alkaline phosphatase-conjugated antibody to digoxigenin, and visualized with the chemiluminescence substrate and X-ray film. p.i., postinfection; Ab, antibody.

Techniques Used: Expressing, Western Blot, Infection, Purification, Northern Blot, Isolation, Staining, Fluorescence, Incubation, Labeling

Viral gene expression and innate immune response in A549 KO cells. (A) Viral protein synthesis. A549 control, RNase L KO, PKR KO, and DKO cells were mock infected or infected with 5 PFU/cell of purified vD10rev, vD9muD10mu, or vΔE3L. At 13 h after infection, the cell lysates were analyzed by Western blotting using rabbit polyclonal antibody to VACV proteins and actin. (B) E3 synthesis. Control and KO A549 cells were mock infected or infected with vD10rev, vD9muD10mu, or vΔE3L in the absence or presence of AraC. The cells were harvested at 2, 4, 8, and 12 h after infection and analyzed by Western blotting with a MAb to E3. (C) rRNA and mRNA. Total RNA was isolated from cells infected as described for panel A and resolved on glyoxal gels. The RNAs were stained with ethidium bromide and detected by UV fluorescence; reverse images are shown. RNAs were transferred from the glyoxal gel to a nylon membrane, incubated with the digoxigenin-labeled probes to the viral late F17 mRNA or cellular GAPDH mRNA, detected with alkaline phosphatase-conjugated antibody to digoxigenin, and visualized with a chemiluminescence substrate on X-ray films. (D) IRF3. Lysates from cells infected as described for panel A were analyzed by Western blotting with antibodies to phosphorylated IRF3, IRF3 protein, and actin. Densities shown below the images were determined with ImageJ.
Figure Legend Snippet: Viral gene expression and innate immune response in A549 KO cells. (A) Viral protein synthesis. A549 control, RNase L KO, PKR KO, and DKO cells were mock infected or infected with 5 PFU/cell of purified vD10rev, vD9muD10mu, or vΔE3L. At 13 h after infection, the cell lysates were analyzed by Western blotting using rabbit polyclonal antibody to VACV proteins and actin. (B) E3 synthesis. Control and KO A549 cells were mock infected or infected with vD10rev, vD9muD10mu, or vΔE3L in the absence or presence of AraC. The cells were harvested at 2, 4, 8, and 12 h after infection and analyzed by Western blotting with a MAb to E3. (C) rRNA and mRNA. Total RNA was isolated from cells infected as described for panel A and resolved on glyoxal gels. The RNAs were stained with ethidium bromide and detected by UV fluorescence; reverse images are shown. RNAs were transferred from the glyoxal gel to a nylon membrane, incubated with the digoxigenin-labeled probes to the viral late F17 mRNA or cellular GAPDH mRNA, detected with alkaline phosphatase-conjugated antibody to digoxigenin, and visualized with a chemiluminescence substrate on X-ray films. (D) IRF3. Lysates from cells infected as described for panel A were analyzed by Western blotting with antibodies to phosphorylated IRF3, IRF3 protein, and actin. Densities shown below the images were determined with ImageJ.

Techniques Used: Expressing, Infection, Purification, Western Blot, Isolation, Staining, Fluorescence, Incubation, Labeling

25) Product Images from "Characterization of chromosome composition of sugarcane in nobilization by using genomic in situ hybridization"

Article Title: Characterization of chromosome composition of sugarcane in nobilization by using genomic in situ hybridization

Journal: Molecular Cytogenetics

doi: 10.1186/s13039-018-0387-z

GISH results of ten S. officinarum clones using biotin labelled S. officinarum genomic DNA and digoxigenin labelled S. spontaneum genomic DNA. a : Badila; b : Loethers; c : Crystallina; d : Muckche; e : Canablanca; f : 50uahapele; g : Luohanzhe; h : Vietnam Niuzhe; i : Nanjian Guozhe; j : Baimeizhe; The chromosomes of S. officinarum show orange-yellow fluorescent, while those of S. spontaneum show green-yellow fluorescent
Figure Legend Snippet: GISH results of ten S. officinarum clones using biotin labelled S. officinarum genomic DNA and digoxigenin labelled S. spontaneum genomic DNA. a : Badila; b : Loethers; c : Crystallina; d : Muckche; e : Canablanca; f : 50uahapele; g : Luohanzhe; h : Vietnam Niuzhe; i : Nanjian Guozhe; j : Baimeizhe; The chromosomes of S. officinarum show orange-yellow fluorescent, while those of S. spontaneum show green-yellow fluorescent

Techniques Used: Clone Assay

26) Product Images from "Molecular Mechanism of Proinflammatory Cytokine-Mediated Squamous Metaplasia in Human Corneal Epithelial Cells"

Article Title: Molecular Mechanism of Proinflammatory Cytokine-Mediated Squamous Metaplasia in Human Corneal Epithelial Cells

Journal: Investigative Ophthalmology & Visual Science

doi: 10.1167/iovs.09-4677

Competitive EMSA analysis of transcription factors on the SPRR1B promoter that mediate the stimulatory effects of IL-1β and IFN-γ. A digoxigenin-labeled, double stranded-DNA probe (60 fM) was added to 5 μg nuclear extract (NE)
Figure Legend Snippet: Competitive EMSA analysis of transcription factors on the SPRR1B promoter that mediate the stimulatory effects of IL-1β and IFN-γ. A digoxigenin-labeled, double stranded-DNA probe (60 fM) was added to 5 μg nuclear extract (NE)

Techniques Used: Labeling

27) Product Images from "A RelA-SpoT homolog (Cr-RSH) identified in Chlamydomonas reinhardtii generates stringent factor in vivo and localizes to chloroplasts in vitro"

Article Title: A RelA-SpoT homolog (Cr-RSH) identified in Chlamydomonas reinhardtii generates stringent factor in vivo and localizes to chloroplasts in vitro

Journal: Nucleic Acids Research

doi:

Genomic structure of Cr-RSH . ( A ) Intronic–exonic organization of Cr-RSH . The gene contains seven exons (open boxes) and six introns (closed boxes). The ORF (open box) and 5′- and 3′-untranslated regions (gray boxes) of the cDNA are also indicated. ( B ) Genomic Southern blot analysis of Cr-RSH . Genomic DNA (3 µg) of C.reinhardtii was digested with Nco I (lane 1), Sac I (lane 2), Sma I (lane 3), Bam HI (lane 4) or Sal I (lane 5), the recognition sites for which in Cr-RSH are shown in (A), and was then probed with digoxigenin-labeled Cr-RSH cDNA. The positions of molecular size standards are shown on the left.
Figure Legend Snippet: Genomic structure of Cr-RSH . ( A ) Intronic–exonic organization of Cr-RSH . The gene contains seven exons (open boxes) and six introns (closed boxes). The ORF (open box) and 5′- and 3′-untranslated regions (gray boxes) of the cDNA are also indicated. ( B ) Genomic Southern blot analysis of Cr-RSH . Genomic DNA (3 µg) of C.reinhardtii was digested with Nco I (lane 1), Sac I (lane 2), Sma I (lane 3), Bam HI (lane 4) or Sal I (lane 5), the recognition sites for which in Cr-RSH are shown in (A), and was then probed with digoxigenin-labeled Cr-RSH cDNA. The positions of molecular size standards are shown on the left.

Techniques Used: Southern Blot, Labeling

28) Product Images from "Effective transfer of chromosomes carrying leaf rust resistance genes from Aegilops tauschii Coss. into hexaploid triticale (X Triticosecale Witt.) using Ae. tauschii × Secale cereale amphiploid forms"

Article Title: Effective transfer of chromosomes carrying leaf rust resistance genes from Aegilops tauschii Coss. into hexaploid triticale (X Triticosecale Witt.) using Ae. tauschii × Secale cereale amphiploid forms

Journal: Journal of Applied Genetics

doi: 10.1007/s13353-014-0264-3

a The scheme of subsequent crosses between Aegilops tauschii × Secale cereale amphiploid forms and triticale cv. Bogo. Hybrids from the generations on distinguished fields were evaluated. b Genomic in situ hybridization (GISH) discrimination of Ae. tauschii chromosomes labeled using digoxigenin-11-dUTP ( green ) and unlabeled triticale chromosomes ( orange ) on meiotic metaphase I chromosome spread of pollen mother cells (PMCs) from the BC 2 F 5 hybrid of ( Aegilops tauschii × Secale cereale ) × triticale, 20” + 1”3D(3B). c Fluorescence in situ hybridization (FISH) pattern showing the location of 5S rDNA ( red ) and 35S rDNA ( green ); d FISH pattern showing the location of pSc119.2 ( green ) and pAs1 ( red ) repetitive clones; and e GISH with a total genomic DNA from rye, R-genome, labeled with rhodamine ( red ); total genomic DNA from Triticum monococcum , A-genome, labeled with digoxigenin and detected by anti-digoxigenin conjugated with FITC ( green / yellow ); and total genomic DNA from Aegilops tauschii , D-genome, labeled with digoxigenin-11-dUTP and tetramethylrhodamine-5-dUTP (ratio 1:1) with blocking genomic DNA of Aegilops speltoides , B-genome (DAPI, blue ) on mitotic, the same chromosome spread of the BC 2 F 5 hybrid of ( Aegilops tauschii × Secale cereale ) × triticale
Figure Legend Snippet: a The scheme of subsequent crosses between Aegilops tauschii × Secale cereale amphiploid forms and triticale cv. Bogo. Hybrids from the generations on distinguished fields were evaluated. b Genomic in situ hybridization (GISH) discrimination of Ae. tauschii chromosomes labeled using digoxigenin-11-dUTP ( green ) and unlabeled triticale chromosomes ( orange ) on meiotic metaphase I chromosome spread of pollen mother cells (PMCs) from the BC 2 F 5 hybrid of ( Aegilops tauschii × Secale cereale ) × triticale, 20” + 1”3D(3B). c Fluorescence in situ hybridization (FISH) pattern showing the location of 5S rDNA ( red ) and 35S rDNA ( green ); d FISH pattern showing the location of pSc119.2 ( green ) and pAs1 ( red ) repetitive clones; and e GISH with a total genomic DNA from rye, R-genome, labeled with rhodamine ( red ); total genomic DNA from Triticum monococcum , A-genome, labeled with digoxigenin and detected by anti-digoxigenin conjugated with FITC ( green / yellow ); and total genomic DNA from Aegilops tauschii , D-genome, labeled with digoxigenin-11-dUTP and tetramethylrhodamine-5-dUTP (ratio 1:1) with blocking genomic DNA of Aegilops speltoides , B-genome (DAPI, blue ) on mitotic, the same chromosome spread of the BC 2 F 5 hybrid of ( Aegilops tauschii × Secale cereale ) × triticale

Techniques Used: In Situ Hybridization, Labeling, Fluorescence, Fluorescence In Situ Hybridization, Clone Assay, Blocking Assay

29) Product Images from "Evolutionary and Experimental Assessment of Novel Markers for Detection of Xanthomonas euvesicatoria in Plant Samples"

Article Title: Evolutionary and Experimental Assessment of Novel Markers for Detection of Xanthomonas euvesicatoria in Plant Samples

Journal: PLoS ONE

doi: 10.1371/journal.pone.0037836

Detection of BSX in infected plant material using an inverted dot blot platform. Crude bacterial suspensions, obtained from tomato and pepper plants leaves after one and two weeks of infection with Xeu 905, were used as templates for PCR enrichment using the markers' primer pairs. PCR products corresponding to each plant were labeled with Digoxigenin and used as probes. Purified DNA from Xeu 905 was used as positive control. Negative controls consisted of tomato plants infected with Pst DC3000 for 2 weeks and uninfected plants. The raw ChemiDoc captures and processed images, using the automatic image analysis algorithm, are shown.
Figure Legend Snippet: Detection of BSX in infected plant material using an inverted dot blot platform. Crude bacterial suspensions, obtained from tomato and pepper plants leaves after one and two weeks of infection with Xeu 905, were used as templates for PCR enrichment using the markers' primer pairs. PCR products corresponding to each plant were labeled with Digoxigenin and used as probes. Purified DNA from Xeu 905 was used as positive control. Negative controls consisted of tomato plants infected with Pst DC3000 for 2 weeks and uninfected plants. The raw ChemiDoc captures and processed images, using the automatic image analysis algorithm, are shown.

Techniques Used: Infection, Dot Blot, Polymerase Chain Reaction, Labeling, Purification, Positive Control

30) Product Images from "Leishmania braziliensis SCD6 and RBP42 proteins, two factors with RNA binding capacity"

Article Title: Leishmania braziliensis SCD6 and RBP42 proteins, two factors with RNA binding capacity

Journal: Parasites & Vectors

doi: 10.1186/s13071-017-2557-y

Analysis of rLbSCD6 and rLbRBP42 binding capacity to the 3′ UTR-II.1-antisense motif. a Secondary structure of the 3′ UTRII.1-antisense motif. Competitive EMSA assays were done using a constant concentration of the rLbSCD6 ( b ) and rLbRBP42 ( c ) proteins and a mixture with both 3′ UTR-II.1-dig and cold antisense ribonucleotides. These mixtures contained a constant concentration of 3′ UTR-II.1-dig ribonucleotide and different amounts (1-, 2-, 4- or 8-fold excess) of the antisense ribonucleotide. In lane labeled ‘0 nM’, the reaction mixture contained the 3′ UTR-II.1-dig ribonucleotide, but the antisense ribonucleotide was not present. To confirm the non-interaction between proteins and the antisense motif, an interaction assay was performance using the digoxigenin-labeled antisense ribonucleotide (lane antisense oligo-dig)
Figure Legend Snippet: Analysis of rLbSCD6 and rLbRBP42 binding capacity to the 3′ UTR-II.1-antisense motif. a Secondary structure of the 3′ UTRII.1-antisense motif. Competitive EMSA assays were done using a constant concentration of the rLbSCD6 ( b ) and rLbRBP42 ( c ) proteins and a mixture with both 3′ UTR-II.1-dig and cold antisense ribonucleotides. These mixtures contained a constant concentration of 3′ UTR-II.1-dig ribonucleotide and different amounts (1-, 2-, 4- or 8-fold excess) of the antisense ribonucleotide. In lane labeled ‘0 nM’, the reaction mixture contained the 3′ UTR-II.1-dig ribonucleotide, but the antisense ribonucleotide was not present. To confirm the non-interaction between proteins and the antisense motif, an interaction assay was performance using the digoxigenin-labeled antisense ribonucleotide (lane antisense oligo-dig)

Techniques Used: Binding Assay, Concentration Assay, Labeling

Analysis of RNA-binding capacity by pull down assays. a Analysis of rLbSCD6. b Analysis of rLbRBP42. Two hundred nanograms of digoxigenin labeled HSP70-II 3′ UTR were incubated with beads containing different amounts of protein. After washing out of the unbound RNA, eluted complexes were deposited on the membrane and the bound RNA was monitored by an antidigoxigenin antibody. RPA1 protein (6.25 pM) was used as a positive control (PC) [ 23 ], and Lbα-tubulin as a negative control (NC)
Figure Legend Snippet: Analysis of RNA-binding capacity by pull down assays. a Analysis of rLbSCD6. b Analysis of rLbRBP42. Two hundred nanograms of digoxigenin labeled HSP70-II 3′ UTR were incubated with beads containing different amounts of protein. After washing out of the unbound RNA, eluted complexes were deposited on the membrane and the bound RNA was monitored by an antidigoxigenin antibody. RPA1 protein (6.25 pM) was used as a positive control (PC) [ 23 ], and Lbα-tubulin as a negative control (NC)

Techniques Used: RNA Binding Assay, Labeling, Incubation, Positive Control, Negative Control

31) Product Images from "Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates"

Article Title: Chromosomal markers in the genus Karenia: Towards an understanding of the evolution of the chromosomes, life cycle patterns and phylogenetic relationships in dinoflagellates

Journal: Scientific Reports

doi: 10.1038/s41598-018-35785-7

Physical mapping of 45S rDNA in three Karenia species. DAPI-stained DNA (blue) and in situ hybridization of the digoxigenin-labeled pTa71 probe for the detection of 45S rDNA (green) in K. brevis ( A–G ), K. selliformis ( H–J ) and K. mikimotoi ( K–Q ) nuclei at different stages of the vegetative cell cycle. In E, the arrow points to a nucleolus at higher magnification to show the co-localization of rDNA in this less-intense DAPI-staining nuclear domain. M–Q provide an example of two-color FISH using the 45S rDNA (green) and (AG) 10 probes (red) before ND-FISH using the telomeric probe. In M, the arrow indicates the AG-chromosome, and the boxes the nuclear areas amplified in N, O and in P, Q to show the precise co-localization of the 45S rDNA (arrows in N, P) with the telomeric signals (arrows in O, Q). Scale bar = 10 μm (A–D, F–M) or 2.5 μm (E, N–Q).
Figure Legend Snippet: Physical mapping of 45S rDNA in three Karenia species. DAPI-stained DNA (blue) and in situ hybridization of the digoxigenin-labeled pTa71 probe for the detection of 45S rDNA (green) in K. brevis ( A–G ), K. selliformis ( H–J ) and K. mikimotoi ( K–Q ) nuclei at different stages of the vegetative cell cycle. In E, the arrow points to a nucleolus at higher magnification to show the co-localization of rDNA in this less-intense DAPI-staining nuclear domain. M–Q provide an example of two-color FISH using the 45S rDNA (green) and (AG) 10 probes (red) before ND-FISH using the telomeric probe. In M, the arrow indicates the AG-chromosome, and the boxes the nuclear areas amplified in N, O and in P, Q to show the precise co-localization of the 45S rDNA (arrows in N, P) with the telomeric signals (arrows in O, Q). Scale bar = 10 μm (A–D, F–M) or 2.5 μm (E, N–Q).

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

32) Product Images from "In Vivo and In Vitro Analyses of Regulation of the Pheromone-Responsive prgQ Promoter by the PrgX Pheromone Receptor Protein"

Article Title: In Vivo and In Vitro Analyses of Regulation of the Pheromone-Responsive prgQ Promoter by the PrgX Pheromone Receptor Protein

Journal: Journal of Bacteriology

doi: 10.1128/JB.00364-12

Binding of purified PrgX to pCF10 DNA templates as determined by electrophoretic mobility shift assay (EMSA). Binding reaction mixtures contained 2.5 nM digoxigenin-labeled DNA probes and various PrgX concentrations. In all three gels shown, “U”
Figure Legend Snippet: Binding of purified PrgX to pCF10 DNA templates as determined by electrophoretic mobility shift assay (EMSA). Binding reaction mixtures contained 2.5 nM digoxigenin-labeled DNA probes and various PrgX concentrations. In all three gels shown, “U”

Techniques Used: Binding Assay, Purification, Electrophoretic Mobility Shift Assay, Labeling

33) Product Images from "GALANIN IS A SELECTIVE MARKER OF THE RETROTRAPEZOID NUCLEUS IN RATS"

Article Title: GALANIN IS A SELECTIVE MARKER OF THE RETROTRAPEZOID NUCLEUS IN RATS

Journal: The Journal of comparative neurology

doi: 10.1002/cne.21897

Galanin-containing neurons co-express Phox2b and VGlut2 but are not catecholaminergic A. PPGal mRNA containing neuron adjacent to B. catecholaminergic neurons revealed with tyrosine hydroxylase (TH) immunoreactivity. C. PPGal mRNA neurons in the RTN co-localize with D. Phox2b immunoreactive (ir) neurons. Arrows point to Phox2b-ir cells that do not contain PPGal mRNA. E. PPGal mRNA neurons revealed with a FITC-labeled riboprobe are co-localized with F. VGlut2 mRNA containing neurons revealed with a digoxigenin-labeled riboprobe. A–B, C–D and E–F are pairs of photomicrographs of the same section taken with either brightfield or fluorescent light. Scale bar in F = 50 microns.
Figure Legend Snippet: Galanin-containing neurons co-express Phox2b and VGlut2 but are not catecholaminergic A. PPGal mRNA containing neuron adjacent to B. catecholaminergic neurons revealed with tyrosine hydroxylase (TH) immunoreactivity. C. PPGal mRNA neurons in the RTN co-localize with D. Phox2b immunoreactive (ir) neurons. Arrows point to Phox2b-ir cells that do not contain PPGal mRNA. E. PPGal mRNA neurons revealed with a FITC-labeled riboprobe are co-localized with F. VGlut2 mRNA containing neurons revealed with a digoxigenin-labeled riboprobe. A–B, C–D and E–F are pairs of photomicrographs of the same section taken with either brightfield or fluorescent light. Scale bar in F = 50 microns.

Techniques Used: Labeling

34) Product Images from "Cell-Specific Expression of Homospermidine Synthase, the Entry Enzyme of the Pyrrolizidine Alkaloid Pathway in Senecio vernalis, in Comparison with Its Ancestor, Deoxyhypusine Synthase 1"

Article Title: Cell-Specific Expression of Homospermidine Synthase, the Entry Enzyme of the Pyrrolizidine Alkaloid Pathway in Senecio vernalis, in Comparison with Its Ancestor, Deoxyhypusine Synthase 1

Journal: Plant Physiology

doi: 10.1104/pp.004259

Northern-blot analysis and RNA loading control of different tissues of S. vernalis . RNA of S. vernalis tissues was hybridized with digoxigenin (DIG)-labeled HSS probe (A) and DHS probe (B) of S. vernalis (buds, lane 1; young leaves, lane 2; young stem, lane 3; flower heads, lane 4; old stem, lane 5; young root, lane 6; and old root, lane 7).
Figure Legend Snippet: Northern-blot analysis and RNA loading control of different tissues of S. vernalis . RNA of S. vernalis tissues was hybridized with digoxigenin (DIG)-labeled HSS probe (A) and DHS probe (B) of S. vernalis (buds, lane 1; young leaves, lane 2; young stem, lane 3; flower heads, lane 4; old stem, lane 5; young root, lane 6; and old root, lane 7).

Techniques Used: Northern Blot, Labeling

35) Product Images from "TrpC3/C7 and Slo2.1 Are Molecular Targets for Metabotropic Glutamate Receptor Signaling in Rat Striatal Cholinergic Interneurons"

Article Title: TrpC3/C7 and Slo2.1 Are Molecular Targets for Metabotropic Glutamate Receptor Signaling in Rat Striatal Cholinergic Interneurons

Journal: The Journal of Neuroscience

doi: 10.1523/JNEUROSCI.0551-07.2007

Expression of TrpC3 and TrpC7, but not TrpC6, in striatal cholinergic interneurons. A , B , TrpC3, TrpC6, and TrpC7 transcripts were detected in horizontal sections through the rat brain by in situ hybridization using [ 33 P]-labeled cRNA probes. A , Film autoradiographs show differential expression of these channels throughout the CNS, with prominent expression of TrpC3 and TrpC7 in hippocampus, cerebellum, cortex, and striatum. B , Left, Within the striatum, a punctate distribution reminiscent of cholinergic interneurons (arrows) was evident for TrpC3 and TrpC7, which was particularly obvious by examination of dark-field images of emulsion-dipped sections. Right, At higher magnification, under bright field, heavy accumulations of silver grains can be seen overlying large neurons (arrows), but not on the more numerous and smaller striatal cells. C , Immunohistochemistry for ChAT (left) was combined with nonisotopic in situ hybridization (right) using digoxigenin-labeled cRNA probes for TrpC3 (top) and TrpC7 (bottom); cholinergic (i.e., ChAT immunoreactive) neurons express both TrpC3 and TrpC7. Scale bars: A , 1 cm; B , left, 200 μm; B , right, C , 50 μm.
Figure Legend Snippet: Expression of TrpC3 and TrpC7, but not TrpC6, in striatal cholinergic interneurons. A , B , TrpC3, TrpC6, and TrpC7 transcripts were detected in horizontal sections through the rat brain by in situ hybridization using [ 33 P]-labeled cRNA probes. A , Film autoradiographs show differential expression of these channels throughout the CNS, with prominent expression of TrpC3 and TrpC7 in hippocampus, cerebellum, cortex, and striatum. B , Left, Within the striatum, a punctate distribution reminiscent of cholinergic interneurons (arrows) was evident for TrpC3 and TrpC7, which was particularly obvious by examination of dark-field images of emulsion-dipped sections. Right, At higher magnification, under bright field, heavy accumulations of silver grains can be seen overlying large neurons (arrows), but not on the more numerous and smaller striatal cells. C , Immunohistochemistry for ChAT (left) was combined with nonisotopic in situ hybridization (right) using digoxigenin-labeled cRNA probes for TrpC3 (top) and TrpC7 (bottom); cholinergic (i.e., ChAT immunoreactive) neurons express both TrpC3 and TrpC7. Scale bars: A , 1 cm; B , left, 200 μm; B , right, C , 50 μm.

Techniques Used: Expressing, In Situ Hybridization, Labeling, Immunohistochemistry

Slo2.1 (Slick) is expressed in striatal cholinergic interneurons. A–D , Nonisotopic in situ hybridization using digoxigenin-labeled antisense ( A , C ) and sense ( B , D ) cRNA probes (left) for Slo2.1 ( A , B ) and Slo2.2 ( C , D ) was combined with immunohistochemistry for ChAT (right) in coronal sections of rat striatum. ChAT-immunopositive striatal cholinergic interneurons labeled with the Slo2.1 probe are indicated (arrows); noncholinergic cortical neurons expressing Slo2.1 are also identified ( A , arrowhead). Slo2.2 labeling was not observed in ChAT-immunoreactive striatal interneurons ( C ; expanded view of the boxed area is provided as an inset). No labeling for Slo2.1 or Slo2.2 was obtained with either of the sense strand control probes. ec, External capsule. Scale bar, 50 μm.
Figure Legend Snippet: Slo2.1 (Slick) is expressed in striatal cholinergic interneurons. A–D , Nonisotopic in situ hybridization using digoxigenin-labeled antisense ( A , C ) and sense ( B , D ) cRNA probes (left) for Slo2.1 ( A , B ) and Slo2.2 ( C , D ) was combined with immunohistochemistry for ChAT (right) in coronal sections of rat striatum. ChAT-immunopositive striatal cholinergic interneurons labeled with the Slo2.1 probe are indicated (arrows); noncholinergic cortical neurons expressing Slo2.1 are also identified ( A , arrowhead). Slo2.2 labeling was not observed in ChAT-immunoreactive striatal interneurons ( C ; expanded view of the boxed area is provided as an inset). No labeling for Slo2.1 or Slo2.2 was obtained with either of the sense strand control probes. ec, External capsule. Scale bar, 50 μm.

Techniques Used: In Situ Hybridization, Labeling, Immunohistochemistry, Expressing

36) Product Images from "Methylation of GPLs in Mycobacterium smegmatis and Mycobacterium avium"

Article Title: Methylation of GPLs in Mycobacterium smegmatis and Mycobacterium avium

Journal: Journal of Bacteriology

doi: 10.1128/JB.186.20.6792-6799.2004

Restriction maps and Southern blot of GPL locus of Myco657 (Δ rmt4 ) and Myco694 (Δ rmt2 ). (A) Genetic arrangement of part of the GPL locus containing rmt2 , rmt4 , rmt3 , and fmt . Positions of the BglII site are shown. The gene names used previously are shown in parentheses. The position where aph was inserted is designated kan . (B) Southern blot of BglII-digested genomic DNA extracted from M. smegmatis mc 2 155, Myco657 (Δ rmt4 ), and Myco694 (Δ rmt2 ). The blot was probed with digoxigenin-labeled DNA corresponding to rmt4 . Gene replacement with aph introduced an additional BglII site, resulting in smaller hybridizing bands for the deletion mutants.
Figure Legend Snippet: Restriction maps and Southern blot of GPL locus of Myco657 (Δ rmt4 ) and Myco694 (Δ rmt2 ). (A) Genetic arrangement of part of the GPL locus containing rmt2 , rmt4 , rmt3 , and fmt . Positions of the BglII site are shown. The gene names used previously are shown in parentheses. The position where aph was inserted is designated kan . (B) Southern blot of BglII-digested genomic DNA extracted from M. smegmatis mc 2 155, Myco657 (Δ rmt4 ), and Myco694 (Δ rmt2 ). The blot was probed with digoxigenin-labeled DNA corresponding to rmt4 . Gene replacement with aph introduced an additional BglII site, resulting in smaller hybridizing bands for the deletion mutants.

Techniques Used: Southern Blot, Labeling

37) Product Images from "Specific In Situ Visualization of the Pathogenic Endophytic Fungus Aciculosporium take, the Cause of Witches' Broom in Bamboo ▿"

Article Title: Specific In Situ Visualization of the Pathogenic Endophytic Fungus Aciculosporium take, the Cause of Witches' Broom in Bamboo ▿

Journal: Applied and Environmental Microbiology

doi: 10.1128/AEM.00635-09

Species-specific visualization of Aciculosporium take by ISH of bamboo shoot tissue. (a) ISH with digoxigenin-labeled oligonucleotide probes on serial cross sections of bamboo bud tissue bearing an A. take ascostroma. Hybridization signals are shown in blue-purple. The A. take -specific probe (Aci65) showed positive signals in fungal structures, including pseudoparenchyma (pp), perithecia (pt), and asci. Furthermore, the signals were shown in intercellular spaces of juvenile leaf (jl) and stem (st). No signal was shown in sheath (sh) and epidermal cells of the stem. The positive control probe (R898) is identical to probe Aci65. The negative control probe (non-Aci65, the complementary sequence of probe Aci65) and no-probe control showed no reaction. Several microphotographs were combined into one large image. Bars, 1 mm. (b to i) ISH with oligonucleotide probe Aci65 on tissues of bamboo shoot colonized by A. take with no external signs of fungal colonization. Positive signals are shown in blue-purple. Magnified views of the boxed regions are shown in c, d, e, g, and i. (b) Longitudinal section of a whole shoot. Several microphotographs were combined into one large image. Bar, 1 mm. (c) Hyphae were observed in the tissue of the fourth lateral bud. Bar, 100 μm. (d) Hyphae were observed in the tissue of the second lateral bud and stem. Bar, 100 μm. (e) Many hyphae were observed in the tissues of the shoot apical meristem (sam) and leaf primordia (lp). Intercellular spaces of the meristem were especially filled with hyphae. Bar, 100 μm. (f) Cross sections of internode stem (st) and sheaths (sh). No signal was detected in sheaths. Bar, 500 μm. (g) Hyphae (arrows) were detected in intercellular spaces of stem. Bar, 100 μm. (h) Cross sections of juvenile leaf. Several hyphae (arrows) were detected in intercellular spaces. Bar, 500 μm. (i) A hypha (arrow) was observed in the intercellular space of the vascular bundle. Bar, 100 μm.
Figure Legend Snippet: Species-specific visualization of Aciculosporium take by ISH of bamboo shoot tissue. (a) ISH with digoxigenin-labeled oligonucleotide probes on serial cross sections of bamboo bud tissue bearing an A. take ascostroma. Hybridization signals are shown in blue-purple. The A. take -specific probe (Aci65) showed positive signals in fungal structures, including pseudoparenchyma (pp), perithecia (pt), and asci. Furthermore, the signals were shown in intercellular spaces of juvenile leaf (jl) and stem (st). No signal was shown in sheath (sh) and epidermal cells of the stem. The positive control probe (R898) is identical to probe Aci65. The negative control probe (non-Aci65, the complementary sequence of probe Aci65) and no-probe control showed no reaction. Several microphotographs were combined into one large image. Bars, 1 mm. (b to i) ISH with oligonucleotide probe Aci65 on tissues of bamboo shoot colonized by A. take with no external signs of fungal colonization. Positive signals are shown in blue-purple. Magnified views of the boxed regions are shown in c, d, e, g, and i. (b) Longitudinal section of a whole shoot. Several microphotographs were combined into one large image. Bar, 1 mm. (c) Hyphae were observed in the tissue of the fourth lateral bud. Bar, 100 μm. (d) Hyphae were observed in the tissue of the second lateral bud and stem. Bar, 100 μm. (e) Many hyphae were observed in the tissues of the shoot apical meristem (sam) and leaf primordia (lp). Intercellular spaces of the meristem were especially filled with hyphae. Bar, 100 μm. (f) Cross sections of internode stem (st) and sheaths (sh). No signal was detected in sheaths. Bar, 500 μm. (g) Hyphae (arrows) were detected in intercellular spaces of stem. Bar, 100 μm. (h) Cross sections of juvenile leaf. Several hyphae (arrows) were detected in intercellular spaces. Bar, 500 μm. (i) A hypha (arrow) was observed in the intercellular space of the vascular bundle. Bar, 100 μm.

Techniques Used: In Situ Hybridization, Labeling, Hybridization, Positive Control, Negative Control, Sequencing

38) Product Images from "Two Distinct Domains in Drosophila melanogaster Telomeres"

Article Title: Two Distinct Domains in Drosophila melanogaster Telomeres

Journal:

doi: 10.1534/genetics.105.048827

TAS on the telomere of the left arm of chromosome 2 . (Left) The 2 L tip region of a polytene chromosome is shown. (Middle) An image of fluorescent in situ hybridization with a 6-kb digoxigenin-labeled DNA probe containing 2 L TAS to the tip of second chromosome
Figure Legend Snippet: TAS on the telomere of the left arm of chromosome 2 . (Left) The 2 L tip region of a polytene chromosome is shown. (Middle) An image of fluorescent in situ hybridization with a 6-kb digoxigenin-labeled DNA probe containing 2 L TAS to the tip of second chromosome

Techniques Used: In Situ Hybridization, Labeling

39) Product Images from "Gustatory Expression Pattern of the Human TAS2R Bitter Receptor Gene Family Reveals a Heterogenous Population of Bitter Responsive Taste Receptor Cells"

Article Title: Gustatory Expression Pattern of the Human TAS2R Bitter Receptor Gene Family Reveals a Heterogenous Population of Bitter Responsive Taste Receptor Cells

Journal: The Journal of Neuroscience

doi: 10.1523/JNEUROSCI.1168-07.2007

In situ hybridizations of human circumvallate papillae using mixed probes specific for pairs of hTAS2Rs. Cross-sections of human circumvallate papillae were hybridized with digoxigenin-labeled antisense probes specific for hTAS2R14 ( A , D ), hTAS2R50 (
Figure Legend Snippet: In situ hybridizations of human circumvallate papillae using mixed probes specific for pairs of hTAS2Rs. Cross-sections of human circumvallate papillae were hybridized with digoxigenin-labeled antisense probes specific for hTAS2R14 ( A , D ), hTAS2R50 (

Techniques Used: In Situ, Labeling

Human TAS2R gene expression in human circumvallate papillae. A , Ten micrometer cross-sections of human circumvallate papillae were hybridized with individual digoxigenin-labeled antisense riboprobes specific for all 25 hTAS2R genes ( A ). Standard colorimetry
Figure Legend Snippet: Human TAS2R gene expression in human circumvallate papillae. A , Ten micrometer cross-sections of human circumvallate papillae were hybridized with individual digoxigenin-labeled antisense riboprobes specific for all 25 hTAS2R genes ( A ). Standard colorimetry

Techniques Used: Expressing, Labeling, Colorimetric Assay

Human TAS2R mRNA is present in a subset of α-gustducin-expressing cells. Dual-color in situ hybridization was done using a digoxigenin-labeled antisense riboprobe specific for human α-gustducin and a fluorescein-labeled antisense riboprobe
Figure Legend Snippet: Human TAS2R mRNA is present in a subset of α-gustducin-expressing cells. Dual-color in situ hybridization was done using a digoxigenin-labeled antisense riboprobe specific for human α-gustducin and a fluorescein-labeled antisense riboprobe

Techniques Used: Expressing, In Situ Hybridization, Labeling

Dual-color in situ hybridizations of selected pairs of bitter receptor mRNAs. A , Dual-color in situ hybridizations were done using digoxigenin-labeled antisense riboprobes and fluorescein-labeled antisense riboprobes for the simultaneous detection of
Figure Legend Snippet: Dual-color in situ hybridizations of selected pairs of bitter receptor mRNAs. A , Dual-color in situ hybridizations were done using digoxigenin-labeled antisense riboprobes and fluorescein-labeled antisense riboprobes for the simultaneous detection of

Techniques Used: In Situ, Labeling

40) Product Images from "An in situ hybridization study of Runx2, Osterix, and Sox9 at the onset of condylar cartilage formation in fetal mouse mandible"

Article Title: An in situ hybridization study of Runx2, Osterix, and Sox9 at the onset of condylar cartilage formation in fetal mouse mandible

Journal:

doi: 10.1111/j.1469-7580.2006.00525.x

Condylar cartilage in coronal plane at E16. Toluidine blue staining (a) and in situ hybridization using digoxigenin-labelled probes (c,e) and 35 S-UTP-labelled probes (b,d,f–i) of a bright field (b) or dark fields (d, f–i). (a) The condylar
Figure Legend Snippet: Condylar cartilage in coronal plane at E16. Toluidine blue staining (a) and in situ hybridization using digoxigenin-labelled probes (c,e) and 35 S-UTP-labelled probes (b,d,f–i) of a bright field (b) or dark fields (d, f–i). (a) The condylar

Techniques Used: Staining, In Situ Hybridization

Condylar anlage in coronal plane at E14. Toluidine blue staining (a) and in situ hybridization using digoxigenin-labelled probes (c,e) and 35 S-UTP-labelled probes (b,d,f–i) of a bright field (b) or dark fields (d,f–i). (a) Although bone
Figure Legend Snippet: Condylar anlage in coronal plane at E14. Toluidine blue staining (a) and in situ hybridization using digoxigenin-labelled probes (c,e) and 35 S-UTP-labelled probes (b,d,f–i) of a bright field (b) or dark fields (d,f–i). (a) Although bone

Techniques Used: Staining, In Situ Hybridization

Condylar anlage in coronal plane at E15. Toluidine blue staining (a) and in situ hybridization using digoxigenin-labelled probes (c,e) and 35 S-UTP-labelled probes (b,d,f–i) of a bright field (b) or dark fields (d, f–i). (a) A metachromatically
Figure Legend Snippet: Condylar anlage in coronal plane at E15. Toluidine blue staining (a) and in situ hybridization using digoxigenin-labelled probes (c,e) and 35 S-UTP-labelled probes (b,d,f–i) of a bright field (b) or dark fields (d, f–i). (a) A metachromatically

Techniques Used: Staining, In Situ Hybridization

Related Articles

DNA Hybridization:

Article Title: Identification of Functional mob Regions in Rhizobium etli: Evidence for Self-Transmissibility of the Symbiotic Plasmid pRetCFN42d
Article Snippet: .. DNA hybridization probes were digoxigenin labeled according to manufacturer instructions (Roche, Barcelona, Spain). .. Hybridization and membrane washes were carried out under high-stringency conditions.

Clone Assay:

Article Title: A novel GAA-repeat-expansion-based mouse model of Friedreich’s ataxia
Article Snippet: .. The probes were prepared using purified DNA from RP11-265B8 and RP11-876N18 BAC clones, which were labelled by nick translation with biotin and digoxigenin, respectively, according to the manufacturer’s instructions (Roche). .. The labelled DNAs were ethanol precipitated together with Cot-1 human DNA (Roche) and resuspended in 10 μl of hybridisation buffer (Sigma).

Isolation:

Article Title: Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development
Article Snippet: .. BAC clone DNA was isolated and labeled with biotin or digoxigenin by using a nick translation kit (Roche). ..

Nick Translation:

Article Title: Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development
Article Snippet: .. BAC clone DNA was isolated and labeled with biotin or digoxigenin by using a nick translation kit (Roche). ..

Article Title: A novel GAA-repeat-expansion-based mouse model of Friedreich’s ataxia
Article Snippet: .. The probes were prepared using purified DNA from RP11-265B8 and RP11-876N18 BAC clones, which were labelled by nick translation with biotin and digoxigenin, respectively, according to the manufacturer’s instructions (Roche). .. The labelled DNAs were ethanol precipitated together with Cot-1 human DNA (Roche) and resuspended in 10 μl of hybridisation buffer (Sigma).

Labeling:

Article Title: Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development
Article Snippet: .. BAC clone DNA was isolated and labeled with biotin or digoxigenin by using a nick translation kit (Roche). ..

Article Title: Identification of Functional mob Regions in Rhizobium etli: Evidence for Self-Transmissibility of the Symbiotic Plasmid pRetCFN42d
Article Snippet: .. DNA hybridization probes were digoxigenin labeled according to manufacturer instructions (Roche, Barcelona, Spain). .. Hybridization and membrane washes were carried out under high-stringency conditions.

Article Title: The Sclerotinia sclerotiorum Mating Type Locus (MAT) Contains a 3.6-kb Region That Is Inverted in Every Meiotic Generation
Article Snippet: .. The probe was labeled with digoxigenin (Roche, Basel, Switzerland) according to the manufacturer’s instructions, and hybridization and detection was performed according to the manufacturer instructions (Roche, Basel, Switzerland). ..

Article Title: High-Throughput Microarray Detection of Vomeronasal Receptor Gene Expression in Rodents
Article Snippet: .. Probes targeting VR were labeled with digoxigenin (Roche, Mannheim, Germany). .. Digoxigenin-labeled probes were detected using BCIP/NBT Color Development Substrate (Promega, Madison, WI) according to the instructions of the manufacturer.

Purification:

Article Title: A novel GAA-repeat-expansion-based mouse model of Friedreich’s ataxia
Article Snippet: .. The probes were prepared using purified DNA from RP11-265B8 and RP11-876N18 BAC clones, which were labelled by nick translation with biotin and digoxigenin, respectively, according to the manufacturer’s instructions (Roche). .. The labelled DNAs were ethanol precipitated together with Cot-1 human DNA (Roche) and resuspended in 10 μl of hybridisation buffer (Sigma).

BAC Assay:

Article Title: Ciona intestinalis Hox gene cluster: Its dispersed structure and residual colinear expression in development
Article Snippet: .. BAC clone DNA was isolated and labeled with biotin or digoxigenin by using a nick translation kit (Roche). ..

Article Title: A novel GAA-repeat-expansion-based mouse model of Friedreich’s ataxia
Article Snippet: .. The probes were prepared using purified DNA from RP11-265B8 and RP11-876N18 BAC clones, which were labelled by nick translation with biotin and digoxigenin, respectively, according to the manufacturer’s instructions (Roche). .. The labelled DNAs were ethanol precipitated together with Cot-1 human DNA (Roche) and resuspended in 10 μl of hybridisation buffer (Sigma).

Hybridization:

Article Title: The Sclerotinia sclerotiorum Mating Type Locus (MAT) Contains a 3.6-kb Region That Is Inverted in Every Meiotic Generation
Article Snippet: .. The probe was labeled with digoxigenin (Roche, Basel, Switzerland) according to the manufacturer’s instructions, and hybridization and detection was performed according to the manufacturer instructions (Roche, Basel, Switzerland). ..

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  • 91
    Roche anti digoxigenin ap antibody
    Patterns of Pax9 , Dkk1 and Dkk2 expression in E13.5 Pax9 +/− and Pax9 −/− palatal shelves suggest that Pax9 is upstream of Wnt signaling. (A,B) Whole-mount lacZ staining (blue) showing that Dkk1 expression is restricted to the posterior domain of palatal shelves in Dkk1 Tg107−lacZ embryos at E13.5 and E14.5. Red dashed lines indicate the boundary of palate. (C,D) Whole-mount in situ hybridization with <t>digoxigenin-labeled</t> probes showing that Dkk2 transcripts (purple) are more visible at the medial edges of the palatal shelves in Pax9 +/+ embryos at E13.5 and E14.5. (E,F) By contrast, Pax9 expression appears stronger and expands along the AP domain of palatal shelves at E13.5 and E14.5. Black dashed lines indicate the position of the sections in G-L. (G-L) In situ hybridizations on adjacent sections, presented in the coronal plane, confirm that Dkk1 (G,H) and Dkk2 (I,J) transcripts have inverse expression patterns with that of Pax9 (K,L) at E13.5 and E14.5. Pax9 expression is more intense along the buccal aspects of palatal mesenchyme (K,L), whereas Dkk2 transcripts localize on the lingual side (I,J). Arrows indicate the higher expression domain. (M-T) In the posterior regions of palatal mesenchyme, Dkk1 (M-P) and Dkk2 (Q-T) expression increased at E13.5 as a result of Pax9 deficiency. B, buccal; L, lingual; T, tongue. n =6 for whole-mount in situ hybridization, n =5 for section in situ hybridization.
    Anti Digoxigenin Ap Antibody, supplied by Roche, used in various techniques. Bioz Stars score: 91/100, based on 34 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche digoxigenin dig labeled rna probes
    CD24 expression in MIN6 cells and analysis of Hepacam2 expression by in situ hybridization. Immunocytochemical analysis (A) and flow cytometric analysis (B) of Pr-LP, Pr-HP, C4-LP, and C4-HP MIN6 cells with an anti-CD24 antibody. CD24 was not detected on the surface of Pr-HP cells. In situ hybridization analysis of Hepacam2 expression in pancreatic islets (C). Pancreatic sections were hybridized with <t>DIG-labeled</t> anti-sense and sense <t>RNA</t> probes for Hepacam2 transcripts (see Materials and Methods ).
    Digoxigenin Dig Labeled Rna Probes, supplied by Roche, used in various techniques. Bioz Stars score: 90/100, based on 10 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche digoxigenin labeled ett putative mar probes
    Summary diagram of GIK regulation and function. The <t>MAR</t> binding protein GIK is directly regulated by the floral homeotic protein AG during reproductive development. GIK modulates and refines the expression of <t>ETT</t> and CRC to control reproductive patterning and JAG and KNU for reproductive differentiation. GIK functions as a multifunctional determinant to coordinate gene expression during reproductive development.
    Digoxigenin Labeled Ett Putative Mar Probes, supplied by Roche, used in various techniques. Bioz Stars score: 85/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Roche digoxigenin dig labeled peua probe
    In vitro translation of <t>peuA</t> mRNA. (A) In vitro translation analysis of the +1 and +39 peuA transcripts labeled with the FLAG tag. The +1- peuA ′- flag RNA and +39- peuA ′- flag RNA were first synthesized by in vitro transcription, as described in the MATERIALS AND METHODS, and a mixture containing either the +1- peuA ′- flag RNA (30 pmol)/ fur - flag RNA (3 pmol) or the +39- peuA ′- flag RNA (30 pmol)/ fur - flag RNA (3 pmol) as the template was subjected to in vitro translation. The FLAG-fused proteins translated were separated on 15% SDS-polyacrylamide gels, and were detected by western blotting using anti-FLAG IgG. (B) Confirmation of the presence of +1- peuA ′- flag RNA and +39- peuA ′- flag RNA in the reaction mixture for in vitro translation. These RNA fragments were detected in the reaction mixture by northern blotting using a <t>DIG-labeled</t> peuA probe.
    Digoxigenin Dig Labeled Peua Probe, supplied by Roche, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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    Image Search Results


    Patterns of Pax9 , Dkk1 and Dkk2 expression in E13.5 Pax9 +/− and Pax9 −/− palatal shelves suggest that Pax9 is upstream of Wnt signaling. (A,B) Whole-mount lacZ staining (blue) showing that Dkk1 expression is restricted to the posterior domain of palatal shelves in Dkk1 Tg107−lacZ embryos at E13.5 and E14.5. Red dashed lines indicate the boundary of palate. (C,D) Whole-mount in situ hybridization with digoxigenin-labeled probes showing that Dkk2 transcripts (purple) are more visible at the medial edges of the palatal shelves in Pax9 +/+ embryos at E13.5 and E14.5. (E,F) By contrast, Pax9 expression appears stronger and expands along the AP domain of palatal shelves at E13.5 and E14.5. Black dashed lines indicate the position of the sections in G-L. (G-L) In situ hybridizations on adjacent sections, presented in the coronal plane, confirm that Dkk1 (G,H) and Dkk2 (I,J) transcripts have inverse expression patterns with that of Pax9 (K,L) at E13.5 and E14.5. Pax9 expression is more intense along the buccal aspects of palatal mesenchyme (K,L), whereas Dkk2 transcripts localize on the lingual side (I,J). Arrows indicate the higher expression domain. (M-T) In the posterior regions of palatal mesenchyme, Dkk1 (M-P) and Dkk2 (Q-T) expression increased at E13.5 as a result of Pax9 deficiency. B, buccal; L, lingual; T, tongue. n =6 for whole-mount in situ hybridization, n =5 for section in situ hybridization.

    Journal: Development (Cambridge, England)

    Article Title: Small-molecule Wnt agonists correct cleft palates in Pax9 mutant mice in utero

    doi: 10.1242/dev.157750

    Figure Lengend Snippet: Patterns of Pax9 , Dkk1 and Dkk2 expression in E13.5 Pax9 +/− and Pax9 −/− palatal shelves suggest that Pax9 is upstream of Wnt signaling. (A,B) Whole-mount lacZ staining (blue) showing that Dkk1 expression is restricted to the posterior domain of palatal shelves in Dkk1 Tg107−lacZ embryos at E13.5 and E14.5. Red dashed lines indicate the boundary of palate. (C,D) Whole-mount in situ hybridization with digoxigenin-labeled probes showing that Dkk2 transcripts (purple) are more visible at the medial edges of the palatal shelves in Pax9 +/+ embryos at E13.5 and E14.5. (E,F) By contrast, Pax9 expression appears stronger and expands along the AP domain of palatal shelves at E13.5 and E14.5. Black dashed lines indicate the position of the sections in G-L. (G-L) In situ hybridizations on adjacent sections, presented in the coronal plane, confirm that Dkk1 (G,H) and Dkk2 (I,J) transcripts have inverse expression patterns with that of Pax9 (K,L) at E13.5 and E14.5. Pax9 expression is more intense along the buccal aspects of palatal mesenchyme (K,L), whereas Dkk2 transcripts localize on the lingual side (I,J). Arrows indicate the higher expression domain. (M-T) In the posterior regions of palatal mesenchyme, Dkk1 (M-P) and Dkk2 (Q-T) expression increased at E13.5 as a result of Pax9 deficiency. B, buccal; L, lingual; T, tongue. n =6 for whole-mount in situ hybridization, n =5 for section in situ hybridization.

    Article Snippet: For whole-mount in situ hybridizations, 2 µg/ml antisense RNA probe was loaded on each sample and the anti-digoxigenin-AP antibody (1:2000) used to detect the labeled probe.

    Techniques: Expressing, Staining, In Situ Hybridization, Labeling, In Situ

    CD24 expression in MIN6 cells and analysis of Hepacam2 expression by in situ hybridization. Immunocytochemical analysis (A) and flow cytometric analysis (B) of Pr-LP, Pr-HP, C4-LP, and C4-HP MIN6 cells with an anti-CD24 antibody. CD24 was not detected on the surface of Pr-HP cells. In situ hybridization analysis of Hepacam2 expression in pancreatic islets (C). Pancreatic sections were hybridized with DIG-labeled anti-sense and sense RNA probes for Hepacam2 transcripts (see Materials and Methods ).

    Journal: PLoS ONE

    Article Title: Microarray Analysis of Novel Candidate Genes Responsible for Glucose-Stimulated Insulin Secretion in Mouse Pancreatic ? Cell Line MIN6

    doi: 10.1371/journal.pone.0061211

    Figure Lengend Snippet: CD24 expression in MIN6 cells and analysis of Hepacam2 expression by in situ hybridization. Immunocytochemical analysis (A) and flow cytometric analysis (B) of Pr-LP, Pr-HP, C4-LP, and C4-HP MIN6 cells with an anti-CD24 antibody. CD24 was not detected on the surface of Pr-HP cells. In situ hybridization analysis of Hepacam2 expression in pancreatic islets (C). Pancreatic sections were hybridized with DIG-labeled anti-sense and sense RNA probes for Hepacam2 transcripts (see Materials and Methods ).

    Article Snippet: Digoxigenin (DIG)-labeled RNA probes were prepared with the DIG RNA Labeling Mix (Cat.#1277073; Roche, Mannheim, Germany) according to the manufacturer's instructions.

    Techniques: Expressing, In Situ Hybridization, Flow Cytometry, Labeling

    Summary diagram of GIK regulation and function. The MAR binding protein GIK is directly regulated by the floral homeotic protein AG during reproductive development. GIK modulates and refines the expression of ETT and CRC to control reproductive patterning and JAG and KNU for reproductive differentiation. GIK functions as a multifunctional determinant to coordinate gene expression during reproductive development.

    Journal: PLoS Biology

    Article Title: AGAMOUS Controls GIANT KILLER, a Multifunctional Chromatin Modifier in Reproductive Organ Patterning and Differentiation

    doi: 10.1371/journal.pbio.1000251

    Figure Lengend Snippet: Summary diagram of GIK regulation and function. The MAR binding protein GIK is directly regulated by the floral homeotic protein AG during reproductive development. GIK modulates and refines the expression of ETT and CRC to control reproductive patterning and JAG and KNU for reproductive differentiation. GIK functions as a multifunctional determinant to coordinate gene expression during reproductive development.

    Article Snippet: The membrane was incubated overnight with 20 ng/mL of digoxigenin-labeled ETT putative MAR probes in DNA binding buffer containing 20 mM Tris-HCl, pH 7.4, 150 mM NaCl, and 20 ng/mL salmon sperm DNA at room temperature, washed, and incubated with anti-dioxigenin coupled with alkaline phosphatase (Roche).

    Techniques: Binding Assay, Expressing

    GIK binds to putative MARs of ETT genomic DNA to modulate its expression. (A) GIK is localized to the nuclear matrix. Nuclear matrix was isolated from the inflorescences of 35S::GIK-GR-6HA plants treated with DEX and harvested 4 h thereafter. Total nuclear and matrix proteins were subjected to western blot analysis. The membrane was first probed with anti-HA to detect GIK and then re-probed with anti-AG. (B) Schematic representation of SMARTest-predicted MARs in the ETT upstream genomic region. Arrow indicates the transcription start site. P1, P2, P3, and P4 are primer pairs used to detect different regions of the ETT genomic DNA used in the ChIP assay. (C) In vitro MAR binding assay of GIK. Left panels, Coomassie Blue staining of a gel loaded with non-induced E. coli containing the wild-type GIK AT-hook motif construct (noninduced), with an IPTG-induced culture containing the construct for the wild-type GIK AT-hook motif (GIK-AT), and with IPTG-induced culture containing a mutated construct in the conserved residues of the GIK AT-hook motif, changing Arg-Gly- Arg -Pro to Arg-Gly- Lys -Pro (GIK-MUT). Right panels, the corresponding south-western results of the MAR binding assay probed with an ETT MAR probe. (D) GIK binds to the MARs of the ETT promoter in vivo. Inflorescences from 35S::GIK-GR-6HA plants treated with DEX were harvested 4 h after DEX induction for ChIP experiments. Anti-HA was used for immunoprecipitation. Relative enrichment was obtained from the ratio of enrichment achieved by anti-HA to that of control IgG. Enrichment of a sequence amplified from the TUB locus was used as a basal control and set to 1.0. P1, P2, P3, and P4 are primer pairs used to detect different regions of the ETT genomic DNA (as illustrated in B). (E, F) Time-course promoter analysis of the ETT gene after GIK induction. 35S::GIK-GR-6HA transgenic plants were crossed with plants transgenic for promoter constructs of wild-type pETT::GUS (E) and pETTΔMAR::GUS with a deletion of distal MARs (F). The inflorescences were treated continuously with DEX every 2 d and harvested for GUS staining at 0, 1, 2, 3, and 4 d after the initial DEX treatment. Upper panels, schematic representations of the ETT upstream genomic region fused with a GUS reporter gene. Lower panels, GUS-stained inflorescences at 0, 1, 2, 3, and 4 d after the initial GIK induction. (G) Time-course analysis of dimethylated-H3K9 level associated with the ETT genomic DNA in 35S::GIK-GR-6HA inflorescences at 0, 2, 4, and 8 h after a single GIK induction. ChIP was performed using anti-dimethylated H3K9 (Upstate). Primer pairs P1, P2, P3, and P4 are shown in Figure 5B . Relative enrichment was obtained from the ratio of bound/input achieved in the respective time points to that at 0 h. The bound/input ratio was first normalized with the bound/input ratio of a basal control, PFK , the transcription of which is not affected by GIK. The enrichment at 0 h was set as 1.0. Standard deviation was obtained from PCR triplicates in D and G.

    Journal: PLoS Biology

    Article Title: AGAMOUS Controls GIANT KILLER, a Multifunctional Chromatin Modifier in Reproductive Organ Patterning and Differentiation

    doi: 10.1371/journal.pbio.1000251

    Figure Lengend Snippet: GIK binds to putative MARs of ETT genomic DNA to modulate its expression. (A) GIK is localized to the nuclear matrix. Nuclear matrix was isolated from the inflorescences of 35S::GIK-GR-6HA plants treated with DEX and harvested 4 h thereafter. Total nuclear and matrix proteins were subjected to western blot analysis. The membrane was first probed with anti-HA to detect GIK and then re-probed with anti-AG. (B) Schematic representation of SMARTest-predicted MARs in the ETT upstream genomic region. Arrow indicates the transcription start site. P1, P2, P3, and P4 are primer pairs used to detect different regions of the ETT genomic DNA used in the ChIP assay. (C) In vitro MAR binding assay of GIK. Left panels, Coomassie Blue staining of a gel loaded with non-induced E. coli containing the wild-type GIK AT-hook motif construct (noninduced), with an IPTG-induced culture containing the construct for the wild-type GIK AT-hook motif (GIK-AT), and with IPTG-induced culture containing a mutated construct in the conserved residues of the GIK AT-hook motif, changing Arg-Gly- Arg -Pro to Arg-Gly- Lys -Pro (GIK-MUT). Right panels, the corresponding south-western results of the MAR binding assay probed with an ETT MAR probe. (D) GIK binds to the MARs of the ETT promoter in vivo. Inflorescences from 35S::GIK-GR-6HA plants treated with DEX were harvested 4 h after DEX induction for ChIP experiments. Anti-HA was used for immunoprecipitation. Relative enrichment was obtained from the ratio of enrichment achieved by anti-HA to that of control IgG. Enrichment of a sequence amplified from the TUB locus was used as a basal control and set to 1.0. P1, P2, P3, and P4 are primer pairs used to detect different regions of the ETT genomic DNA (as illustrated in B). (E, F) Time-course promoter analysis of the ETT gene after GIK induction. 35S::GIK-GR-6HA transgenic plants were crossed with plants transgenic for promoter constructs of wild-type pETT::GUS (E) and pETTΔMAR::GUS with a deletion of distal MARs (F). The inflorescences were treated continuously with DEX every 2 d and harvested for GUS staining at 0, 1, 2, 3, and 4 d after the initial DEX treatment. Upper panels, schematic representations of the ETT upstream genomic region fused with a GUS reporter gene. Lower panels, GUS-stained inflorescences at 0, 1, 2, 3, and 4 d after the initial GIK induction. (G) Time-course analysis of dimethylated-H3K9 level associated with the ETT genomic DNA in 35S::GIK-GR-6HA inflorescences at 0, 2, 4, and 8 h after a single GIK induction. ChIP was performed using anti-dimethylated H3K9 (Upstate). Primer pairs P1, P2, P3, and P4 are shown in Figure 5B . Relative enrichment was obtained from the ratio of bound/input achieved in the respective time points to that at 0 h. The bound/input ratio was first normalized with the bound/input ratio of a basal control, PFK , the transcription of which is not affected by GIK. The enrichment at 0 h was set as 1.0. Standard deviation was obtained from PCR triplicates in D and G.

    Article Snippet: The membrane was incubated overnight with 20 ng/mL of digoxigenin-labeled ETT putative MAR probes in DNA binding buffer containing 20 mM Tris-HCl, pH 7.4, 150 mM NaCl, and 20 ng/mL salmon sperm DNA at room temperature, washed, and incubated with anti-dioxigenin coupled with alkaline phosphatase (Roche).

    Techniques: Expressing, Isolation, Western Blot, Chromatin Immunoprecipitation, In Vitro, Binding Assay, Staining, Construct, In Vivo, Immunoprecipitation, Sequencing, Amplification, Transgenic Assay, Standard Deviation, Polymerase Chain Reaction

    In vitro translation of peuA mRNA. (A) In vitro translation analysis of the +1 and +39 peuA transcripts labeled with the FLAG tag. The +1- peuA ′- flag RNA and +39- peuA ′- flag RNA were first synthesized by in vitro transcription, as described in the MATERIALS AND METHODS, and a mixture containing either the +1- peuA ′- flag RNA (30 pmol)/ fur - flag RNA (3 pmol) or the +39- peuA ′- flag RNA (30 pmol)/ fur - flag RNA (3 pmol) as the template was subjected to in vitro translation. The FLAG-fused proteins translated were separated on 15% SDS-polyacrylamide gels, and were detected by western blotting using anti-FLAG IgG. (B) Confirmation of the presence of +1- peuA ′- flag RNA and +39- peuA ′- flag RNA in the reaction mixture for in vitro translation. These RNA fragments were detected in the reaction mixture by northern blotting using a DIG-labeled peuA probe.

    Journal: PLoS ONE

    Article Title: Regulation of the Expression of the Vibrio parahaemolyticus peuA Gene Encoding an Alternative Ferric Enterobactin Receptor

    doi: 10.1371/journal.pone.0105749

    Figure Lengend Snippet: In vitro translation of peuA mRNA. (A) In vitro translation analysis of the +1 and +39 peuA transcripts labeled with the FLAG tag. The +1- peuA ′- flag RNA and +39- peuA ′- flag RNA were first synthesized by in vitro transcription, as described in the MATERIALS AND METHODS, and a mixture containing either the +1- peuA ′- flag RNA (30 pmol)/ fur - flag RNA (3 pmol) or the +39- peuA ′- flag RNA (30 pmol)/ fur - flag RNA (3 pmol) as the template was subjected to in vitro translation. The FLAG-fused proteins translated were separated on 15% SDS-polyacrylamide gels, and were detected by western blotting using anti-FLAG IgG. (B) Confirmation of the presence of +1- peuA ′- flag RNA and +39- peuA ′- flag RNA in the reaction mixture for in vitro translation. These RNA fragments were detected in the reaction mixture by northern blotting using a DIG-labeled peuA probe.

    Article Snippet: The digoxigenin (DIG)-labeled peuA probe was prepared with a primer pair, VppeuA-F/VppeuA-R (see ), internal to the peuA gene using a DIG PCR Probe Synthesis Kit (Roche).

    Techniques: In Vitro, Labeling, FLAG-tag, Synthesized, Western Blot, Northern Blot