Telesis 2021

Front Matter: This edition of Telesis, the University of Oklahoma Gibbs College of Architecture student journal, explores the theme of "Isolation."Editorial: The Telesis Team introduces Telesis: Isolation.Association: Randall Kinnaman shares his childhood experiences of visiting his incarcerated father at various prison visitation centers.Disorientation: Giuliana Vaccarino Gearty explores the positive outcomes from feeling lost in a city.Dismantling: Travis Howell and Tanner Pickens share the history of Oklahoma City’s Deep Deuce and Interstate 235.Engagement: Kate O’Connor introduces Marywood University’s Socially Responsible Architecture seminar.Food Fight: Rebecca Doglas combats food deserts.Drops: Ian Goodale provides shelter to the homeless.Displacement: Ben Gravel provides shelter for those displaced by California Wildfires.Schematics: Ryan Godfrey proposes inclusive design schematics for people with autism.Villa: Candelaria Mas Pohmajevic examines COVID 19 outbreaks in Argentina’s Shanty Towns.Rehabilitation: David Swaby investigates prison rehabilitation in the form of educational programs.Chair: Jake Lange explores the importance of agency in processes of rehabilitation.Incarceration: Emily Hays calls designers to no longer be complicit in the design of carceral facilities.Tunnel: Johanna Hilmes explores the benefits of incorporating color in prison design.Interview: Alex Finklestein interviews Dr. Jae James regarding his experience of incarceration and resultant ambitions.N

Rapid genome mapping in nanochannel arrays for highly complete and accurate de novo sequence assembly of the complex Aegilops tauschii genome.

Next-generation sequencing (NGS) technologies have enabled high-throughput and low-cost generation of sequence data; however, de novo genome assembly remains a great challenge, particularly for large genomes. NGS short reads are often insufficient to create large contigs that span repeat sequences and to facilitate unambiguous assembly. Plant genomes are notorious for containing high quantities of repetitive elements, which combined with huge genome sizes, makes accurate assembly of these large and complex genomes intractable thus far. Using two-color genome mapping of tiling bacterial artificial chromosomes (BAC) clones on nanochannel arrays, we completed high-confidence assembly of a 2.1-Mb, highly repetitive region in the large and complex genome of Aegilops tauschii, the D-genome donor of hexaploid wheat (Triticum aestivum). Genome mapping is based on direct visualization of sequence motifs on single DNA molecules hundreds of kilobases in length. With the genome map as a scaffold, we anchored unplaced sequence contigs, validated the initial draft assembly, and resolved instances of misassembly, some involving contigs <2 kb long, to dramatically improve the assembly from 75% to 95% complete

Deletion of incorrect contigs in genome map-guided <i>de novo</i> sequence assembly.

<p>The original assembly contained two Nt.BspQI sites and ∼8 kb of sequence that were absent from the genome map. The top image is output from gsAssembler and shows the scaffolding of contigs using paired-end reads. The green line represents the sequence coverage for each region. Paired-end reads are represented by pink (high coverage) and aqua (low coverage) carrots (□). The three contigs with red bars beneath them contain the extra sequence motifs and total sequence consistent with the predicted incorrect scaffold. They also contain weak paired-end data indicating that the contigs are misplaced. The bottom line shows the sequence assembly after deletion of the three contigs with red bars.</p

Comparison of the final genome map guided sequence assembly to the genome map.

<p>The final sequence assembly almost completely spans the genome map. Gaps in the genome map are denoted with asterisks.</p

Contig assembly error identification through genome map comparison.

<p>The top line represents the <i>in silico</i> map for the original sequence assembly, the majority of which is covered by a single sequence contig. The genome map matches on the left and right sides of the contig (shown with shaded boxes). ∼3 kb of sequence was incorrectly inserted into the contig during assembly.</p

Comparison of the sequence assembly scaffold to the genome map.

<p>The sequence assembly is shown with dark grey boxes representing sequence contigs. Contigs were bridged by paired-end sequence reads. The genome map is represented by light grey boxes. Shaded boxes around regions of both maps denote regions where the sequence assembly matches the genome map well. Regions where there are significant discrepancies are numbered and discussed in the results section. The two gaps in the genome map are denoted with asterisks.</p

Identification and assembly of repeat sequences in genome map-guided <i>de novo</i> sequence assembly.

<p>Panel A shows the strip diagram for one of the clones that covers the high density region, each line represents a different molecule and the spots are the location of green (Nt.BspQI) labels. Two high-density label regions are marked “label repeats,” and they do not cluster into discrete peaks. Panel B shows a pairwise alignment of the high-density region after reassembly based on the genome map. The alignment shows two blocks of direct repeats which are inverted with respect to one another. Panel C shows the original assembly on the top, the genome map in the middle and the final assembly on the bottom, containing the repeat sequence as predicted by the genome map.</p

Two-color genome mapping with two enzymes.

<p>A. The DNA backbone is stained with YOYO-1 and loaded into the port of a nanochannel array chip. The DNA molecules are introduced into the region with pillars and micron-scale relaxation channels by an electric field where they unwind and linearize. Finally, they are moved into the 45 nm nanochannels, where they stretch uniformly to 85% of the length of perfectly linear B-DNA. B. Linearized BAC DNA molecules in nanochannels. The DNA molecule is stained with YOYO-1, and Nt.BspQI and Nt.BbvCI nicks are labeled with green and red dyes, respectively. C. Molecule length and nick locations are extracted from the images by custom image-analysis software. By clustering individual molecules with high similarity of green label patterns, distinct patterns are extracted (top panel). The locations of the red labels are then overlaid on the green label patterns (middle pattern). A histogram plot of the above clusters is shown in the bottom panel. The peaks represent the location of each sequence motif (GCTCTTC and CCTCAGC) along the linearized DNA molecules. D. Consensus maps for individual BAC clones are shown. Consensus maps are combined by using overlapping patterns, and the final genome map is shown at the bottom. E. The clone map from genome mapping is shown at the top and the full genome map as a grey bar with Nt.BspQI and Nt.BbvCI motif locations in green and red. Below the genome map, in blue, is the physical map from SNaPshot fingerprinting. The total length of the genome map is 2.1 Mb.</p