Journal: Cell Cycle

Article Title: Genomic and chromatin features shaping meiotic double-strand break formation and repair in mice

doi: 10.1080/15384101.2017.1361065

Figure Lengend Snippet: Crossover asymmetry in hotspots with polymorphisms in putative PRDM9 binding sites. (A) Model for crossover asymmetry. A sequence polymorphism in a PRDM9 binding site may affect relative DSB frequencies on the 2 hotspot alleles, manifested as asymmetry in the locations of crossover breakpoints. If DSBs are preferentially formed on the B6 chromosome of a B6 × DBA hybrid mouse, crossover breakpoints will tend to lie to the left of the hotspot center when recombinant products are assayed after PCR amplification in the B6-to-DBA orientation, and will tend to lie to the right when amplified in the DBA-to-B6 orientation. (B and C) Examples of crossover hotspots with (B) or without (C) crossover asymmetry. (i) B6 (top) and DBA (bottom) sequences of putative 36-bp binding sites for PRDM9 B6 at hotspot centers. The nucleotides shaded in yellow in HS59.5 highlight a polymorphism between the B6 and DBA haplotypes. In HS61.1 , the PRDM9 motif shown is on the Crick strand. (ii) SPO11-oligo maps. Red lines indicate SPO11-oligo hotspots. (iii) Crossover breakpoints (densities expressed as centiMorgans (cM) per Mb) mapped by allele-specific PCR on sperm DNA in the B6-to-DBA (top) and DBA-to-B6 (bottom) orientation. , Ticks represent tested polymorphisms. (iv) Cumulative distributions of crossover breakpoints with fitted Gaussian curves. The number indicates the distance between the 2 curves at the midpoint for each cumulative plot. Vertical dashed lines indicate hotspot centers. For hotspot HS61.1 , zero values in both orientations at outlier position -1130 bp are not shown. (D) Crossover asymmetry is associated with presence of polymorphisms in putative PRDM9 binding sites at hotspots (Table S3). Crossover asymmetry was defined for each locus as the absolute difference between the midpoints of cumulative crossover breakpoint maps in the 2 orientations.

Article Snippet: For crossover breakpoint analyses, cumulative breakpoint distributions with fitted Gaussian curves were determined using GraphPad Prism version 7.

Techniques: Binding Assay, Sequencing, Recombinant, Amplification

Journal: Frontiers in Computational Neuroscience

Article Title: Detecting global form: separate processes required for Glass and radial frequency patterns

doi: 10.3389/fncom.2013.00053

Figure Lengend Snippet: Example stimuli are depicted as described in the text. Judgments were made regarding the center of rotation of the Glass pattern relative to the black outer Gaussian markers.

Article Snippet: The data was fit with a cumulative Gaussian (Prism 4.0, Graphpad Software Inc., 2005) using the following variant of Equation 3: (4) Y = 0.5 { 1 + e r f [ x − P S A σ 2 ] } where Y = proportion of responses to the right, erf = error function, x = amount of displacement, PSA = point of subjective alignment, and σ = the standard deviation of the fitted cumulative Gaussian.

Techniques: