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Gallus BioPharmaceuticals
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Gallus BioPharmaceuticals
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OriGene
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Image Search Results
Journal: eLife
Article Title: A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes
doi: 10.7554/eLife.19993
Figure Lengend Snippet: Comparison of the genomic region containing Gcna in mouse (GRCm38/mm10) with syntenic regions in human (GRCh38/hg38), rabbit (Broad/oryCun2), opossum (Broad/monDom5), chicken (ICGSC Gallus_gallus-4.0/galGal4), zebrafish (Zv9/danRer7), and elephant shark (Callorinchus_milii-6.1.3/calMil1). Gcna orthologs are indicated in green. DOI: http://dx.doi.org/10.7554/eLife.19993.009
Article Snippet: Comparison of the genomic region containing
Techniques: Comparison
Journal: eLife
Article Title: A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes
doi: 10.7554/eLife.19993
Figure Lengend Snippet: ( A ) Domain composition of rodent GCNA proteins. Rabbit, which diverged from rodents 80 million years ago, serves as an outgroup. ( B ) Mouse and rat genomes contain non-transcribed pseudo-exons encoding structured domains. Human metalloprotease and zinc finger domains (encoded by human exons 10–12 and 12–13, respectively) aligned with translations of the corresponding mouse and rat non-transcribed exon remnants. Identical residues are indicated by stars, strongly similar residues by colons, and weakly similar residues by periods according to the Gonnet PAM 250 matrix (ClustalW). Dashes represent gaps in the alignment. Stop codons are indicated by red boxes and frameshifts by carets. Regions are color coded as follows: zinc metalloprotease-like (blue), zinc finger (purple), and HMG box (pink). The coordinates of the pseudo-exons in the mouse GRCm38/mm10 release are as follows (numbered according to corresponding human exons): exon 9 (ChrX: 101707035–101707103), exon 10 (ChrX: 101721392–101721498), exon 11 (ChrX: 101724005–101724133), exon 12 (ChrX: 101725798–101726001), and exon 13 (ChrX: 101727141–101727423). The coordinates of the pseudo-exons in rat RGSC 6.0/m6 are: exon 9 (ChrX: 71604116–71604175) and exon 10 (ChrX: 71610020–71610164). Sequences corresponding to human exons 11- 13 are not found in the rat genome. Note: primates have an in-frame stop codon before the HMG box (exon 13). DOI: http://dx.doi.org/10.7554/eLife.19993.010
Article Snippet: Comparison of the genomic region containing
Techniques:
Journal: eLife
Article Title: A widely employed germ cell marker is an ancient disordered protein with reproductive functions in diverse eukaryotes
doi: 10.7554/eLife.19993
Figure Lengend Snippet: ( A ) Maximum likelihood phylogenetic tree showing relationships among eukaryotic GCNA, Wss1, Spartan, and bacterial SprT protease domains. GCNA, Wss1, and Spartan are present across eukarya, including the most primitive eukaryotes, except that Wss1 proteins have been lost in animals. Gray and black circles indicate nodes with bootstrap values greater than 600 and 900 (out of 1000), respectively. Tree is based on alignment of the protease domains and was created with PhyML. ( B ) Structural modeling of GCNA, Wss1, and Spartan protease domains places GCNA in the minigluzincin family of proteases along with Wss1 and Spartan. Pairwise protein structure comparison using FATCAT detected strong structural similarity, as evidenced by small root-mean-square deviations (RMSDs), which are measures of the average distance (in Angstroms) between the carbon atoms of the superimposed proteins. All structures were found to be significantly similar. DOI: http://dx.doi.org/10.7554/eLife.19993.024
Article Snippet: Comparison of the genomic region containing
Techniques: Comparison
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: A.Scheme of Rtn4 circRNA sequence localization in the Rtn4 gene and CircRNA expression cassette from pCircRNA-BE and pCircRNA-DMo vectors; mouse Rtn4 circRNA consists exon 2 and exon 3 of Rtn4 gene. 800 nts inverted repeats (purple colour) in the flanking introns were constructed to promote back-splicing through forming inter-intronic base-pairing; the flanking introns lacks 5’ and 3’ splice site respectively which would abolish the classic splicing of exon 2 and exon 3; chimeric intron was shown in green; & and #, the Rtn4 circRNA RT-PCR oligo positions; &, Rtn4-c-R, Rtn4-c-F were used in qRT-PCR to determine Rtn4 circRNA levels (results shown in B); #, Rtn4-VR, Rtn4-VF were used to verify Rtn4 circRNA back-splicing fidelity (results shown in C); *, the position of northern blot probe oligo (Rtn4-NB-R1) used in D. B.Rtn4 circRNA expression levels in transfected cells (HeLa, N2a, N2a-swe.10, HEK293 cell); Control = pCMV-MIR empty vector; BE-Rtn4 = pCircRNA-BE-Rtn4; DMo-Rtn4 = pCircRNA-DMo-Rtn4; All statistic T tests were performed by comparison with the control sample, *** *, P ≤ 0.0001, n ≥ 4; β-Actin mRNA was used as internal control. C.Agarose gel electrophoresis of RT-PCR products of Rtn4 circRNA to verify back-splicing fidelity (PCR primers: Rtn4-VR, Rtn4-VF); Control = pCMV-MIR empty vector; BE-Rtn4 = pCircRNA-BE-Rtn4; DMo-Rtn4 = pCircRNA-DMo-Rtn4. The entire un-spliced primary precursor transcript is about 5.3 k nt; the spliced circular form of Exon 2 and exon 3 without intron is 2.4 k nt. The size of Intron between two exons is 818 nt. The expected amplicon size is 2.4 kb. As the products migrated between 2.0 and 2.5 kb, proving that the internal intron was spliced out in Rtn4 circRNA biogenesis. lane 1-3, HeLa cells; lane 4-6, N2a cells; lane 7-9, N2a-swe.10 cells; lane 10-12, HEK293 cells. PCR products were sequenced and aligned (data not shown). D.Northern blot of Rtn4 circRNA in transfected HEK293 cells. Control-1 = pCMV-MIR empty vector; Rtn4-Exon2-Exon3 = pCMV-Rtn4-Exon2-Exon3; Control-2, the construct without inverted repeat at 3’ flanking intronic region; BE-Rtn4 = pCircRNA-BE-Rtn4; DMo-Rtn4 = pCircRNA-DMo-Rtn4; -, no RNase R treatment; +, with RNase R treatment; ethidium bromide staining of agarose gel showing 28S and 18S rRNAs were used as loading control. E.Sequencing of junction site of back-splicing of Rtn4 circRNA overexpressed in N2a and HEK293 cells. The RT-PCR products from C were sequenced and the junction regions were shown; RT-PCR product-4, 5, 6 were from N2a cell; RT-PCR product-11, 12 were from HEK293 cell.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: Sequencing, Expressing, Construct, Reverse Transcription Polymerase Chain Reaction, Quantitative RT-PCR, Northern Blot, Transfection, Plasmid Preparation, Agarose Gel Electrophoresis, Amplification, Staining
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: GPP expression from SV40 promoter in each circRNA expression plasmid DNA transfection in HEK293 cell was measured by western blot analysis with antibody against GFP. β-Actin was used as loading control. Control, pCircRNA-DMo; BE-Rtn4, pCircRNA-BE-Rtn4; DMo-Rtn4, pCircRNA-DMo-Rtn4; DMo-Rtn4-FLAG, pCircRNA-DMo-Rtn4-FLAG; DMo-Rtn4-Stop, pCircRNA-DMo-Rtn4-Stop; PAT1-Rtn4, pCircRNA-PAT1-Rtn4; IVS1-Rtn4, pCircRNA-IVS1-Rtn4.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: Expressing, Plasmid Preparation, Transfection, Western Blot
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: A. Scheme of the Rtn4 circRNA expression cassette for pCircRNA-IVS1-Rtn4 and pCircRNA-PAT1-Rtn4 constructs. IVS1 intron was shown in red colour and PAT1 intron was shown in blue colour. B. Rtn4 circRNA expression in N2a cells after transfection with Rtn4 circRNA constructs. All statistic T tests were performed by comparison with the control sample, *** *, P ≤ 0.0001, ** *, P ≤ 0.001, n ≥ 4.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: Expressing, Construct, Transfection
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: A.Scheme illustrating the insertion of a FLAG tag and stop codon into exon 2 of the open reading frame of Rtn4 circRNA. Blue, open reading frame; green arrow, start codon, the first AUG in the ORF; yellow arrow, FLAG tag in the pCircRNAsDMo-Rtn4-FLAG construct; red rectangle, stop codon (UGA) in the pCircRNA-DMo-Rtn4-Stop construct. B. Indefinite open reading frame (ORF) of Rtn4 circRNA. Start codon, AUG in the ORF. C. Western blot of Rtn4 circRNA translated proteins in HEK293 cell detected by antibodies against Nogo-A (α-Nogo-A). Control, empty vector; BE-Rtn4 = pCircRNA-BE-Rtn4; DMo-Rtn4 = pCircRNA-DMo-Rtn4; Rtn4-Exon2-Exon3 = pCMV-Rtn4-Exon2-Exon3. On the right repeating peptides are multimers of the Rtn4 circRNA translation product; RTN4-fl indicates the endogenous RTN4 full length protein (Nogo-A); monomer was the single round translation product of Rtn4 circRNA. The calculated MW of monomer is 88.2 kDa. As it has very acidic pI (4.3), which may cause it migrate larger to 150 kDa position . D. Open reading frame of Rtn4-FLAG circRNA. The aspartic acid (blue D) is translated from the junction site of back-splicing; FLAG tag was inserted in exon 2; the blue E is the translated from junction site of exon2-exon3; the green M is translated from start codon. E. Western blot of pCircRNA-DMo-Rtn4-FLAG transfected N2a cells using an anti-FLAG antibody (α-FLAG). Control, the empty vector; DMo-Rtn4-FLAG = pCircRNA-DMo-Rtn4-FLAG; off-note, compared to C, the intensity of repeating peptides is higher than monomer; the reason is unknown, possibly due to the different antibody affinity between multimer and monomer. F. Open reading frame of Rtn4-stop circRNA; red rectangle, stop codon (UGA). G. Western blot of pCircRNA-DMo-Rtn4-Stop transfected HEK293 cells using an anti-Nogo A antibody (α-Nogo-A). Control, the empty vector; DMo-Rtn4-Stop = pCircRNA-DMo-Rtn4-Stop; DMo-Rtn4 = pCircRNA-DMo-Rtn4. H. Mass spectrometry results of Rtn4 circRNA derived peptides (Rtn4-circRNA-DP) expressed in HEK293 cell. The predicted sequence of monomer mouse Rtn4 circRNA derived peptides; red sequences, the detected peptides (detailed peptide spectrometry was provided in ). I. Mass spectrometry results of immunoprecipitation of Rtn4-FLAG circRNA derived peptides (Rtn4-FLAG-circRNA-DP) expressed in N2a cell. Black sequences, undetected peptides; 76.8% amino acids are detected in mass spectrometry (shown in red); Blue D was the translated amino acid from the junction site of back-splicing, which is the direct evidence of translation from Rtn4-FLAG-circRNA; blue E is the translation product of junction site formed after the removal of the internal intron between exon2 and exon3; light blue I is the last amino acid of one round transition; green M is from the start codon (AUG); peptides labelled with underline were the junction peptides; detected peptides with dotted line was the direct evidence of rolling circle translation of Rtn4-FLAG-circRNA; arrow indicates continuous repeating translation. J. Mass spectrometry of peptide labelled with underline in I; the direct evidence of the protein translation from the junction site of back-splicing of Rtn4. K. Mass spectrometry of peptide labelled with dotted line in I; the direct evidence of the continuous translation of Rtn4 circRNA which generate repeating peptides. L. Open reading frame of Rtn4-FLAG-ac circRNA; ac, adenosine and cytosine; red rectangle, stop codon (UAA). M. Western blot analysis of pCircRNA-DMo-Rtn4-ac transfected in N2a cells using an anti-Nogo A antibody (α-Nogo-A). DMo-Rtn4-FLAG = pCircRNA-DMo-Rtn4-FLAG; DMo-Rtn4-FLAG-ac = pCircRNA-DMo-Rtn4-FLAG-ac.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: FLAG-tag, Construct, Western Blot, Plasmid Preparation, Transfection, Mass Spectrometry, Derivative Assay, Sequencing, Immunoprecipitation
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: 17 mass spectrums of the tryptic peptides of Rtn4 circRNA derived protein Left ordinate is the relative intensity, right ordinate is the absolute intensity, Horizontal ordinate is m/z.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: Derivative Assay
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: Alignment of RTN4 circRNA derived protein sequences from mouse and human. The sequences of mouse Rtn4 circRNA derived protein (Mouse_Rtn4_circRNA-DP) and human Rtn4 circRNA derived protein (human_Rtn4_circRNA-DP) were aligned through ClustalX2.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: Derivative Assay
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: A. Western blot with Anti-Nogo A antibody of N2a cells with Rtn4 circRNA overexpression. Control, empty vector; BE-Rtn4, pCircRNA-BE-Rtn4; DMo-Rtn4, pCircRNA-DMo-Rtn4; IVS1-Rtn4, pCircRNA-IVS1-Rtn4; PAT1-Rtn4, pCircRNA-PAT1-Rtn4; DMo-Rtn4-FLAG, pCircRNA-DMo-Rtn4-FLAG; DMo-Rtn4-Stop, pCircRNA-DMo-Rtn4-Stop; the high molecular weight bands bigger than 250 kDa represent the repeating peptides from Rtn4 circRNA continuous translation; monomer is the single round Rtn4 circRNA translation product; actin is used as loading control. B. the longer explosion of the high molecular weight bands bigger than 250 kDa.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: Western Blot, Over Expression, Plasmid Preparation, Molecular Weight
Journal: bioRxiv
Article Title: Intron-mediated enhancement boosts Rtn4 circRNA expression: A robust method for exploring circRNA function
doi: 10.1101/257105
Figure Lengend Snippet: Human brain frontal lobe and mouse frontal cortex samples were fractioned by SDS-PAGE and immunoblotted against Nogo-A (α-Nogo-A). RTN4-fl, RTN4 full length protein (Nogo-A); monomer, monomer of RTN4 circRNA derived peptide; repeating peptides, multimer of RTN4 circRNA derived peptide. β-Actin was used as a loading control.
Article Snippet: To construct the Rtn4 circRNA expression plasmid,
Techniques: SDS Page, Derivative Assay
Journal: Atherosclerosis
Article Title: Confirmation of Ath26 locus on chromosome 17 and identification of Cyp4f13 as an atherosclerosis modifying gene
doi: 10.1016/j.atherosclerosis.2019.05.007
Figure Lengend Snippet: (A) Correlation between lesion area and Cyp4f13 gene expression in BMDM from F2 male mice (n=114, r=0.46, r2=0.21, p<0.0001). (B) F2 male mice were divided into three genotypes AA (n=24), AD (n=62), DD (n=27) at the Cyp4f13 locus. BMDM from three genotypes were cultured and Cyp4f13expression was determined microarray (p values <0.001 by ANOVA analysis with Tukey posttest). (C) Cyp4f13 gene expression assessed by qPCR in BMDM from the DBA/2J WT, Het and KO as well as AKR/J mice (n=3 to 4 biological replicates, different letters above the bars represent p<0.05 by ANOVA with Tukey posttest). (D) Aortic root lesion areas confirm the Ath26 QTL in female congenic mice on the AKR background. The genotype of the chr 17 interval is designated as homozygous for DBA/2 (DD, n=8), heterozygous (AD, n=10), and homozygous for AKR (AA, n=17) (*, p<0.05; ***, p<0.001 by nonparametric ANOVA with Dunns posttest).
Article Snippet: Real-time PCR assay was performed with Applied Biosystems TaqMan Universal PCR Master Mix and Taqman probe Mouse Chr 17:
Techniques: Gene Expression, Cell Culture, Microarray
Journal: Atherosclerosis
Article Title: Confirmation of Ath26 locus on chromosome 17 and identification of Cyp4f13 as an atherosclerosis modifying gene
doi: 10.1016/j.atherosclerosis.2019.05.007
Figure Lengend Snippet: (A) WT and Cyp4f13 KO BMDM 24 hour migration after scratch wound in response to LTB4 (300 nM) or 15% serum-containing media. Migration distance was measured at multiple positions along multiple scratches for each condition (medium ± interquartile range, >100 measurements made for each condition, different letters above the data represent columns with p<0.05 by nonparametric ANOVA with Dunns posttest). (B) Cholesterol efflux from WT and Cyp4f13 KO BMDM to apoA1 and HDL acceptors (n=4 for each condition). (C-E) Total, free, and esterified cholesterol levels in unloaded (open bars) and AcLDL loaded (gray bars) WT and Cyp4f13 KO BMDM, normalized to cell protein (n= 4 per condition). For (B-D), **, p<0.01; ***, p<0.001 by parametric ANOVA with Newman–Keuls posttest.
Article Snippet: Real-time PCR assay was performed with Applied Biosystems TaqMan Universal PCR Master Mix and Taqman probe Mouse Chr 17:
Techniques: Migration
Journal: Atherosclerosis
Article Title: Confirmation of Ath26 locus on chromosome 17 and identification of Cyp4f13 as an atherosclerosis modifying gene
doi: 10.1016/j.atherosclerosis.2019.05.007
Figure Lengend Snippet: (A) Representative aortic root lesions stained with Oil red O and hematoxylin in 16 week old chow-diet fed female DBA/2 Apoe−/− mice of the indicated Cyp4f13 genotype. (B). Aortic root lesion areas in female (left panel) and male (right panel) mice for the indicated Cyp4f13 genotypes. Parametric ANOVA p-values are shown above the data using Tukey’s posttest analysis. For the male mice, one WT and one Het values were excluded based on the pre-specified >2 S.D. outlier rule. (C) Representative aortic root lesions stained for macrophages (left panel, CD68 immunofluorescence in red), smooth muscle cells (center panel, alpha actin immunofluorescence in red), and with hematoxylin (right panel) in order to determine lesion cellular composition and necrosis. Blue shows nuclei stained with DAPI, and green shows autofluorescence of the elastic lamina. (D) Quantification of macrophage (left panel), smooth muscle cell (middle panel), and necrotic (right panel) relative lesion areas (n=7 to 9 lesions per genotype, *, p<0.05).
Article Snippet: Real-time PCR assay was performed with Applied Biosystems TaqMan Universal PCR Master Mix and Taqman probe Mouse Chr 17:
Techniques: Staining, Immunofluorescence
Journal: Atherosclerosis
Article Title: Confirmation of Ath26 locus on chromosome 17 and identification of Cyp4f13 as an atherosclerosis modifying gene
doi: 10.1016/j.atherosclerosis.2019.05.007
Figure Lengend Snippet: Plasma cholesterol values in Apoe −/− mice by sex and Cyp4f13 genotypes.
Article Snippet: Real-time PCR assay was performed with Applied Biosystems TaqMan Universal PCR Master Mix and Taqman probe Mouse Chr 17:
Techniques: Clinical Proteomics