Journal: Scientific Reports

Article Title: PARTICLE triplexes cluster in the tumor suppressor WWOX and may extend throughout the human genome

doi: 10.1038/s41598-017-07295-5

Figure Lengend Snippet: Predicted PARTICLE consensus structure and triplex formation with one local enrichment at the WWOX tumor suppressor locus on chromosome 16. ( A ) Secondary structure minimum free energy (MFE) prediction of PARTICLE in human (left) and mouse (right) with LocARNA consensus pairing (centre; compatible base pairs are colored). ( B ) Schematics of the WWOX locus on human chromosome 16 and mouse chromosome 8 (upper, exons in blue boxes) and predicted triplex binding sites (yellow boxes) with PARTICLE (vertical lines, lower). ( C ) GENCODE hg19 assembly with PARTICLE triplex sites on plus (red) and minus (blue) genomic strands as identified by Triplexator v1.3.2. The genomic location of tumor suppressors MAT2A and WWOX are indicated. ( D ) Percentage of triplex binding sites (involving PARTICLE regions 1098–1114 nucleotides (white), 629–646 nucleotides (grey) and 624–644 nucleotides (black)) and ( E ) PARTICLE triplex frequency per megabase on all human chromosomes combined (All), chromosome 2 (Ch2) and 16 (Ch16) and within the WWOX locus. Human silhouette (id:47607240, Dreamstime.com).

Article Snippet: A local consensus RNalifold structure was generated from aligned human PARTICLE : NR_038942.1 and mouse PARTICLE : 4930414L22Rik sequences using LocARNA ( http://rna.informatik.uni-freiburg.de ) .

Techniques: Binding Assay

Journal: Microorganisms

Article Title: Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)

doi: 10.3390/microorganisms7110493

Figure Lengend Snippet: Secondary structure features of the Pseudokeronopsis ITS2 molecule. ( A ) Consensus secondary structure predicted using the LocARNA Sever. Color bars (0–1) indicate base-pairing probability. ( B ) Structural model for Pseudokeronopsis . ( C ) Helix A structures of congeners. Using the structure of P. carnea as a reference, compensating base changes (CBCs) are marked with filled arrows and hemi-CBCs are indicated with hollow arrows. The variable region is marked by a grey box. Newly sequenced species are in bold. *, misidentified.

Article Snippet: Consensus structures of Pseudokeronopsis ITS2 and LSU-D2 regions (Figures 3A and 5A) were predicted using the LocARNA Sever with default options (available from http://rna.informatik.uni-freiburg.de/LocARNA/Input.jsp ) [ ].

Techniques:

Journal: Microorganisms

Article Title: Ciliate Environmental Diversity Can Be Underestimated by the V4 Region of SSU rDNA: Insights from Species Delimitation and Multilocus Phylogeny of Pseudokeronopsis (Protist, Ciliophora)

doi: 10.3390/microorganisms7110493

Figure Lengend Snippet: Secondary structure features of the Pseudokeronopsis LSU-D2 molecule. ( A ) Consensus secondary structure predicted using the LocARNA Sever. Color bars (0–1) indicate base-pairing probability. ( B ) Helix II structures of congeners. Using the structure of P. songi as a reference, CBCs are marked with filled arrows and hemi-CBCs are indicated with hollow arrows. The variable regions are marked by grey boxes. Newly sequenced species are in bold. *, misidentified species.

Article Snippet: Consensus structures of Pseudokeronopsis ITS2 and LSU-D2 regions (Figures 3A and 5A) were predicted using the LocARNA Sever with default options (available from http://rna.informatik.uni-freiburg.de/LocARNA/Input.jsp ) [ ].

Techniques: