Journal: Journal of Virology

Article Title: Genome Structure and Thymic Expression of an Endogenous Retrovirus in Zebrafish

doi: 10.1128/JVI.78.2.899-911.2004

Figure Lengend Snippet: Expression of ZFERV-related RNA in thymus. (A) Larval fish at 5 dpf were fixed and subjected to whole mount in situ hybridization with a DIG-labeled sense or antisense probe for the env gene, followed by colorimetric detection. (B and C) Contiguous sections (20 μm thick) of 3-month-old fish (right two panels) were subjected to in situ hybridization with probes as described in panel A. The section planes and main organs are indicated. Abbreviations: B, brain; E, esophagus; G, gill; H, heart; I, intestine; L, liver; M, muscle; T, thymus. The bilateral thymi hybridizing to the antisense probe are highlighted with arrows. (D) Sections (2 μm thick) of the thymus from 3-month-old fish were hybridized to fluorescein-labeled sense (left panel) or antisense (right panel) env probe, followed by fluorescence detection with the alkaline phosphatase-Fast Red system.

Article Snippet: For hybridization, samples were incubated with prehybridization buffer (4× SSC [600 mM NaCl, 60 mM sodium citrate; pH 7], 50% [vol/vol] formamide) at 37°C for 10 min, followed by incubation at 42°C for 16 h in hybridization buffer (50% [vol/vol] formamide, 4× SSC, 1× Denhardt solution [200 mg/liter each for Ficoll 400, polyvinylpyrrolidone, and bovine serum albumin], 100 μg of heparin/ml, 0.1% Tween 20, 1 mg of yeast Torula RNA [Sigma]/ml) containing fluorescein- or digoxigenin [DIG]-labeled RNA probe (0.2 μg/ml).

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

Journal: Scientific Reports

Article Title: Deterioration of willow seeds during storage

doi: 10.1038/s41598-018-35476-3

Figure Lengend Snippet: ( A ) Nucleases and RNAses were activated in the presence or absence of Ca 2+ (left), and of Zn 2+ (right). Double-stranded (ds) and single-stranded (ss) DNA and RNA were used as substrates. Total proteins were extracted and analyzed at the indicated pH values. ( B ) DNA and protein contents during storage. Numbers 1, 2, and 3 correspond to seeds collected in 2016, 2006 and 2000, respectively. ( C ) Progressive DNA fragmentation can be seen: in the three lanes, one band of high molecular weight allows identifying the non-fragmented DNA; in lanes 2 and 3, DNA smearing and two diffuse bands lower than 600 bp (around 360 and 180 bp) are detected in lanes 2 and 3 (red arrows), m = marker. Mean ± s.d. values followed by different letters are significantly different according to the ANOVA test at P

Article Snippet: Protein extracts from different harvest times were resolved on 12% SDS-PAGE gels containing herring sperm DNA (Biodynamics, Argentina) or torula yeast RNA (Sigma Aldrich, Merck, Darmstadt, Germany).

Techniques: Molecular Weight, Marker

Journal: Chemical Science

Article Title: Violation of DNA neighbor exclusion principle in RNA recognition of DNA neighbor exclusion principle in RNA recognition †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5sc03740a

doi: 10.1039/c5sc03740a

Figure Lengend Snippet: Experimental and theoretically calculated fluorescence spectra. (a) Fluorescence of tRNA from baker's yeast (10 μM), probes 1–3 (10 μM) and probes 1–3 with tRNA from baker's yeast. (HEPES buffer pH = 7.4, slit width = 5 nm) (b) fluorescence of RNA from torula yeast (10 μM), probes 1–3 (10 μM), probes 1–3 with RNA from torula yeast and fluorescence of probe 1 with tRNA (GCGCGCGCGC and AUAUAUAUAU). (HEPES buffer pH = 7.4, slit width = 5 nm) (c) fluorescence of probe 1 (10 μM) in the presence of RNA, denatured RNA, F – , Cl – , heme, glucose, ssDNA, dsDNA, UTP, TTP, ATP, GTP and CTP (10 equiv.) (HEPES buffer pH = 7.4, slit width = 5 nm). (d) Fluorescence results from TD-DFT calculations.

Article Snippet: Sodium salts of ATP, GTP, CTP, TTP and UTP, heme, glucose, dsDNA (from Calf Thymus), RNA (from baker's yeast) and RNA (from torula yeast) were also purchased from Aldrich and used without further purification.

Techniques: Fluorescence

Journal: Life

Article Title: Amphiphilic Compounds Assemble into Membranous Vesicles in Hydrothermal Hot Spring Water but Not in Seawater

doi: 10.3390/life8020011

Figure Lengend Snippet: Lauric acid–glycerol monolaurate (LA–GML, 10 mM) was mixed with yeast ribosomal RNA in a 2:1 ratio by weight in pH 3.3 Geyser Basin water, then dried on a microscope and rehydrated with the same volume of water. Phase ( A ) and fluorescence ( B ) images. ( C ) A control in which the same lipid mixture was prepared without a wet–dry cycle and put through the gel permeation column in the absence of RNA.

Article Snippet: To test encapsulation of nucleic acids, LA–GML was mixed in a 2:1 ratio by weight with either Torula yeast ribosomal RNA (CHEM-IMPEX Int’l Inc. Wood Dale, IL) or with lambda phage DNA.

Techniques: Microscopy, Fluorescence