The Lantern, 2013-2014

• Strikes • Pietro di Venezia • To the Lover of Small Things • Jim\u27s Big Day • Akademiks • Redamancy • A Love Poem for Arctia Caja • Mother River • The Lyrics to Your Song • Nerves • Gemini Season • White Interface • The Last Time I Played with Dolls • The Mechanic • My Goldfish • Put Down Your Hammer • Strip • Hollywood • Identity • The Grey Zone • Sophia • When I Became a Poet • Unbroken • The Veteran Aeronaut • I Have Running Water but They had the Stars • Not A Nigga • Mother, Adam, Eve • From Fragile Seeds: A Palindrome • Conspiring, The Spires • Finally Working Out What Goes Where (God, For Example, is in His Kingdom) • Identity Crisis • Affection • Patience • An Enchanting Lost Cause • False Starts • Soggy Rice, Lukewarm Water • The Glow • Heat • 9-14 • Filigree • Diane Arbus • Touched • Dying Alive • Just Another Drunkard on the Train • Dinner • The French Legionnaire • Conspiracy and Theory • 1249am • Colored Pencils • Sea Glass • Roundtrip • The Muse Heard Music • Lacrimosa • The Allegory of the Maze • The Stars on Stuart Road • To Isabella • For Want of a Potato Chip • Termite Nests • Saving a Rose • Today and Yesterday • A Foggy New York • Cat; Wurtzburg • Embrace • Faces • Geisha • Pacis Leo • Patterns • Te-Whanganui-a-Tara (The Dock)https://digitalcommons.ursinus.edu/lantern/1180/thumbnail.jp

\u3ci\u3eDrosophila\u3c/i\u3e Muller F Elements Maintain a Distinct Set of Genomic Properties Over 40 Million Years of Evolution

The Muller F element (4.2 Mb, ~80 protein-coding genes) is an unusual autosome of Drosophila melanogaster; it is mostly heterochromatic with a low recombination rate. To investigate how these properties impact the evolution of repeats and genes, we manually improved the sequence and annotated the genes on the D. erecta, D. mojavensis, and D. grimshawi F elements and euchromatic domains from the Muller D element. We find that F elements have greater transposon density (25–50%) than euchromatic reference regions (3–11%). Among the F elements, D. grimshawi has the lowest transposon density (particularly DINE-1: 2% vs. 11–27%). F element genes have larger coding spans, more coding exons, larger introns, and lower codon bias. Comparison of the Effective Number of Codons with the Codon Adaptation Index shows that, in contrast to the other species, codon bias in D. grimshawi F element genes can be attributed primarily to selection instead of mutational biases, suggesting that density and types of transposons affect the degree of local heterochromatin formation. F element genes have lower estimated DNA melting temperatures than D element genes, potentially facilitating transcription through heterochromatin. Most F element genes (~90%) have remained on that element, but the F element has smaller syntenic blocks than genome averages (3.4–3.6 vs. 8.4–8.8 genes per block), indicating greater rates of inversion despite lower rates of recombination. Overall, the F element has maintained characteristics that are distinct from other autosomes in the Drosophila lineage, illuminating the constraints imposed by a heterochromatic milieu