Journal:

Article Title: Disruption of Gammaherpesvirus 68 Gene 50 Demonstrates that Rta Is Essential for Virus Replication

doi: 10.1128/JVI.77.10.5731-5739.2003

Figure Lengend Snippet: Genomic structure of gene 50 recombinant viruses. (A) Southern blot analysis. (Left) wt, G50.Stop.[Frt-Kan-Frt], and G50.Stop.Frt BAC viral genomes were purified from E. coli DH10B cells, digested with SpeI, electrophoresed, blotted, and hybridized with a biotin-labeled gene 50 probe (bp 66642 to 69462). The biotin-labeled gene 50 probe was generated by using the Detector random primer DNA biotinylation kit (Kirkegaard & Perry Laboratories), and the Southern blot was developed by using the DNA Detector genomic Southern blotting kit (Kirkegaard & Perry Laboratories) according to the manufacturer's instructions. (Right) wt γHV68 or wt BAC and G50.Stop.Frt BAC (G50 KO in the text) viral genomes were purified from virions isolated from NIH 3T12 and gene 50-expressing stable cell line 14.29, respectively, digested with XbaI, electrophoresed, blotted, and hybridized with a 32P-labeled gene 44 probe (bp 61444 to 62183). On both panels, the fragment sizes of the molecular size markers are shown to the left of each blot (1-kb DNA ladder for the left panel, lambda DNA-BstEII digest for the right panel; New England Biolabs). To the right of each blot are shown the predicted sizes of the viral DNA fragments detected by the respective probes in each blot. (B) Nucleotide sequence of the region containing the mutation in the G50.Stop.Frt BAC. The genome coordinates are to the right of the nucleotide sequence. The nucleotide sequence shown in lowercase letters denotes the gene 50 intron of the spliced gene 50 transcript, and the sequence in uppercase letters denotes the second gene 50 exon of the spliced gene 50 transcript. The splice acceptor site is denoted with an arrowhead. The ORF 50 ATG is boxed. The mutation in G50.Stop.Frt BAC is depicted in boldface, the introduced TAG stop codon is boxed, the FRT site is underlined, and the XbaI site within the FRT site is boxed and italicized.

Article Snippet: The biotin-labeled gene 50 probe was generated by using the Detector random primer DNA biotinylation kit (Kirkegaard & Perry Laboratories), and the Southern blot was developed by using the DNA Detector genomic Southern blotting kit (Kirkegaard & Perry Laboratories) according to the manufacturer's instructions. (Right) wt γHV68 or wt BAC and G50.Stop.Frt BAC (G50 KO in the text) viral genomes were purified from virions isolated from NIH 3T12 and gene 50-expressing stable cell line 14.29, respectively, digested with Xba I, electrophoresed, blotted, and hybridized with a 32 P-labeled gene 44 probe (bp 61444 to 62183).

Techniques: Recombinant, Southern Blot, Purification, Labeling, Generated, Isolation, Expressing, Stable Transfection, Lambda DNA Preparation, Sequencing, Mutagenesis

Journal: Nucleic Acids Research

Article Title: Cloning and expression of new microRNAs from zebrafish

doi: 10.1093/nar/gkl278

Figure Lengend Snippet: Cloning frequency and conservation for all miRNAs cloned from zebrafish small-RNA cDNA libraries. The upper panel depicts the cloning frequency for all small RNAs that were found in the two libraries and that passed our computational pipeline. All 139 known miRNAs (blue data points) were cloned more than once, while 37 out of the 66 new miRNAs (pink dots) were represented by a single sequenced clone. The lower panel shows a scatter plot of the conservation of known (blue dots) and new (pink data dots) miRNAs in 12 vertebrate species (zebrafish, fugu, tetraodon, mouse, rat, human, dog, macaca, opossum, chicken, chimpanzee, cow). Forty-four of the new miRNAs were only found in zebrafish, while most of the known miRNAs were found in several species according to our conservation criteria.

Article Snippet: Two small-RNA cDNA libraries were prepared by Vertis Biotechnologie AG (Freising-Weihenstephan, Germany).

Techniques: Cloning, Clone Assay

Journal: medRxiv

Article Title: Polymorphism in IFNAR contributes to glucocorticoid response and outcome in ARDS and COVID-19

doi: 10.1101/2022.03.10.22272123

Figure Lengend Snippet: (A ) STAT1 expression in the lung after 4-day culture in the presence of IFN beta with or without hydrocortisone (HC). ( B) pSTAT1 expression in the same specimens as in A. ( C) Example photomicrographs showing higher STAT2 expression in a TT patient than in a CT patient and the effect of HC on its nuclear translocation. Most STAT2 remains in the cytoplasm of the CT patients, whereas nuclear expression is prominent in the TT patient. Indicated insets are shown in the bottom row. Arrows. ( D ) Combined results of all patients noting that two CT samples are excluded in the data as the patients were already under glucocorticoid treatment at the time of sample acquisition. Ns, not significant; *P<0.05; **P<0.01; and ***P<0.001

Article Snippet: The first stage antibodies were anti-alpha chain of the IFN alpha/beta receptor (St John’s Laboratory STJ112765) that was used 1:2000 and 1:5000 and anti-Stat1 (1:400, 9175S), anti-pStat1(1:100, 9167S) and anti-Stat2 (1:200, 72604S) all from Cell Signalling.

Techniques: Expressing, Translocation Assay