Journal: Journal of Fish Biology

Article Title: Identification of a gene set to evaluate the potential effects of loud sounds from seismic surveys on the ears of fishes: a study with Salmo salar

doi: 10.1111/jfb.12398

Figure Lengend Snippet: Summary of microarray and quantitative reverse transcription–polymerase chain reaction (qRT-PCR) analyses of microarray-identified transcripts

Article Snippet: The cDNA targets were mixed with 2 μl of LNA dT blocker, 3 μl of GFP spike and 35 μl of 2× formamide-based hybridization buffer (25% formamide, 4× SSC, 0·5% SDS, 2× Denhardt's solution) (Genisphere) and hybridized to the pre-warmed arrays by application of 22 mm × 60 mm HybriSlip coverslips (Grace Biolabs; www.gracebio.com ), in microarray hybridization chambers (Corning; www.corning.com ) in a 50° C water bath for 16 h in the dark.

Techniques: Microarray, Reverse Transcription Polymerase Chain Reaction, Sequencing, Quantitative RT-PCR

Journal: The Journal of biological chemistry

Article Title: Biochemical analysis of mutant T7 primase/helicase proteins defective in DNA binding, nucleotide hydrolysis, and the coupling of hydrolysis with DNA unwinding.

doi: 10.1074/jbc.271.43.26825

Figure Lengend Snippet: FIG. 8. Cross-section of the hexamer ring with five 4B and one 4A subunit. The larger, top domain is the C terminus helicase domain. The smaller, middle domain is the N terminus primase domain, and the smallest, bottom domain is the zinc-binding domain, which is only present on the 4A subunit, needed for primase template recognition. The 60-mer ssDNA is shown binding through the hexamer hole, and the directionality is indicated. Possible interactions with the DNA-binding site, located inside the hole, explain the requirement of a tail flanking the 39 side of the primase template sequence. The 60-mer DNA image was constructed using the HyperChem program; the 4B hexamer image was provided by Dr. Egelman (University of Minnesota) and derived from electron microscopic analysis, and the 63-amino acid zinc-binding domain was drawn to scale and placed in its most likely position.

Article Snippet: Reactions were quenched with 1 N HCl and chloroform at various time intervals, from 0 to 60 min. After neutralization to pH 7 with 1 M Tris base, 1 M NaOH, the samples were mixed with an equal volume of sequencing gel loading buffer (95% formamide and 0.05% bromphenol blue) and applied to a 25% polyacrylamide, 3% bisacrylamide, 3 M urea sequencing gel (Bio-Rad apparatus; 35 3 43 cm 3 0.2 mm thickness).

Techniques: Binding Assay, Sequencing, Construct, Derivative Assay

Journal: The Journal of biological chemistry

Article Title: Biochemical analysis of mutant T7 primase/helicase proteins defective in DNA binding, nucleotide hydrolysis, and the coupling of hydrolysis with DNA unwinding.

doi: 10.1074/jbc.271.43.26825

Figure Lengend Snippet: FIG. 9. Possible structure of 4A* helicase domain. The predicted secondary structure of 4A9 is aligned with the known structure of the F1-ATPase as described in the text. The numbers indicate the beginning and ending residues of each secondary structural element. Boxes represent a-helices, and arrows represent b-sheets. The helicase-conserved motifs are indicated above the 4A9 sequence. Above the 4A9 structure, black arrows indicate the positions of group A mutants K318A, E348K, D424N, and S496F. White arrows indicate the position of group B mutants R487C and G488D. Gray arrows indicate the position of the group C mutants S345F and G451E. Above the F1-ATPase structure, downward pointing arrows indicate the position of amino acid residues that interact with the nucleotide bound primarily on the b subunit. Upward pointing arrows indicate the position of amino acid residues that interact with the nucleotide bound primarily on the adjacent a subunit. The location of Walker A and B nucleotide binding motifs and the R-loop are indicated above the structure.

Article Snippet: Reactions were quenched with 1 N HCl and chloroform at various time intervals, from 0 to 60 min. After neutralization to pH 7 with 1 M Tris base, 1 M NaOH, the samples were mixed with an equal volume of sequencing gel loading buffer (95% formamide and 0.05% bromphenol blue) and applied to a 25% polyacrylamide, 3% bisacrylamide, 3 M urea sequencing gel (Bio-Rad apparatus; 35 3 43 cm 3 0.2 mm thickness).

Techniques: Sequencing, Binding Assay

Journal: Bangladesh Journal of Pharmacology

Article Title: Detection of cytosolic tRNA in mammal by Northern blot analysis

doi: 10.3329/bjp.v12i3.32501

Figure Lengend Snippet: Figure 2: Northern blot for detection of methionine initiator tRNA. Equal amounts (30 μg) of RNA sample was resolved on a denaturing urea polyacrylamide gel and subjected to either EDC based chemical crosslinking or traditional UV based crosslinking after electro-blotting to the nylon membrane

Article Snippet: Exposure cassette and intensifier screen (GE Healthcare) REAGENTS AND SOLUTIONS o Urea (ultra-pure, Sigma-Aldrich, Catalog No. U6504) o 40% Polyacrylamide solution (Bio-Rad, 29:1 3.3% crosslinker, Catalog No. 161-0146) o N,N,N’,N’-Tetramethylethylenediamine (TEMED, C6H16N2) (Sigma-Aldrich, Catalog No. T9281) o 10 % Ammonium persulfate (APS, (NH4)2S2O8) (Sigma-Aldrich, Catalog No. A3678) o Formamide (Bio Basic Canada Inc. CAS-75-12-7) o Diethylpyrocarbonate (DEPC, O(COOC2H5)2) (Bio World, SKU: 40400024-3) o Xylene Cyanol FF (C25H27N2NaO6S2) (Sigma-Aldrich, Catalog Number: x-4126) o Bromophenol Blue (C9H10Br4O5S) (Sigma-Aldrich, Catalog No. 114391) o Tris Base (Bio Basic Canada, CAS-77-86-1) o Boric Acid (Bio Basic Canada, CAS-10043-35-3) o EDTA (Daejung, Catalog No. 60-00-4) o DNA probe oligonucleotides o Mammalian cytosolic methionine initiator tRNA (TRX-CAT1-1 gene) probe sequence

Techniques: Northern Blot, Western Blot, Membrane