The Ursinus Weekly, December 13, 1973

J. Board reactivates; Tries first case in three years • Service project going well as U.C. students aid area children • Special correspondent tells tale of wonder and awe • Mr. Xaras says art is necessary • Nine Ursinus students selected for Who’s Who • Editorial: A step in the right direction; What happened to Thanksgiving? • Letters to the editor: Is sex necessary?; Where is the mail?; Responsibility and the Ursinus woman; A disapproval; Respect for science; Basement telephone; Morning noises; Breaking the rule • B. Dale Davis, from bulletin, speaks at forum • The Stage: The second shepherd’s play • Faculty Portrait: Charles T. Sullivan, psychology teacher • The Zodiac: Fate or free will? The Zodiac vs. magic • Donald F. Zucker speaks to meeting of Socratic club • Sermon on the monstrosity • Final exam schedule • Four straight victorieshttps://digitalcommons.ursinus.edu/weekly/1008/thumbnail.jp

The Ursinus Weekly, October 5, 1972

Jerrold Schecter speaks on China: Mao in control • Ursinus administration appoints twelve new faculty members for coming year • Voting deadline nears; Have you registered? • News editors hope for expansion and diversity • Editorial: A falling star? • Focus: Andrea Turner • Ursinus receives a big fat government grant • Coordinating the freshmen, or Thank God for the relay races • Tired of classes? • Harriers upset by DelVal; Win streak ends • Soccer team impressive in Villanova victory • New coach takes over • Gridders drop first two to F&M, Lebanon Valley • Sports buffs\u27 corner • Sports scoreboardhttps://digitalcommons.ursinus.edu/weekly/1086/thumbnail.jp

The Ursinus Weekly, November 1, 1973

UN Day held at UC • USGA-Union lock horns over new rep. position • SFARC elections held; warning system set • Protheatre productions scheduled for weekend • Musicians initiated into Pi Nu Epsilon • Editorial: The American Film Theatre; New furniture in Wilkinson lounge • Letters to the editor: Jazz fan responds; Starving student complains; Mr. Self speaks • Alumni corner • Jazz: Herman Herd in motion • Faculty Portrait: Dr. Peter G. Jessup • A discourse on mental divorce • Billy Jack • Ursinus downs U of P; then falls to Rams • Bears lose fifth game to a tough Widener teamhttps://digitalcommons.ursinus.edu/weekly/1004/thumbnail.jp

The Ursinus Weekly, February 14, 1974

Week-long festival of arts slated to begin February 22 • Ursinus, at mid-winter, continues coping with problems of energy conservation • Forums set for semester • ProTheatre to present evening of avant-garde • Villanova University to sponsor tenth law review symposium • Editorial: The Myrin follies; Situation wanted: Hero • First semester Dean’s List • Letters to the editor: Union anniversary; Madison Avenue\u27s effect • Student teachers respond to experiences in area schools • SFARC News • Film Review: The Exorcist • Alumni Corner: Mike Hunter: Society drop-in • De-horn the Rams! • Jazz: Thad Jones, Mel Lewis • USGA holds elections, makes amendments and forms committees • 9-5 and still alive!https://digitalcommons.ursinus.edu/weekly/1009/thumbnail.jp

The Ursinus Weekly, November 15, 1973

First SFARC meeting yields suggestions for parking, Wismer • Banana split rated big success as news spreads across the country • Philadelphia soloists will play at forum • Career day planned for English majors • New Sturgis portrait dedicated at ceremony • Editorial: All that shivers is not cold • Spotlight: Mr. Scott Dempsey • Letters to the editor: SFARC member pledges interest; Faculty digs banana split • Alumni corner: U.C. graduate now holds position as ambassador • Tolstoy’s War and peace to be shown on PBS starting next Tuesday • Jazz: Buddy Rich strikes out • Believe it or not • A splendid time was guaranteed for all • The Zodiac: A preview to real astrology • Guard hired to check I.D.’s during open dorms • Ursinus women athletes make better lovers • Booters stand 6-6-1 • X-country wrap-up • Bears upset Grove Cityhttps://digitalcommons.ursinus.edu/weekly/1006/thumbnail.jp

Using Phylogenetically-Informed Annotation (PIA) to search for light-interacting Genes in Transcriptomes from Non-Model Organisms

Background: Tools for high throughput sequencing and de novo assembly make the analysis of transcriptomes (i.e. the suite of genes expressed in a tissue) feasible for almost any organism. Yet a challenge for biologists is that it can be difficult to assign identities to gene sequences, especially from non-model organisms. Phylogenetic analyses are one useful method for assigning identities to these sequences, but such methods tend to be time-consuming because of the need to re-calculate trees for every gene of interest and each time a new data set is analyzed. In response, we employed existing tools for phylogenetic analysis to produce a computationally efficient, tree-based approach for annotating transcriptomes or new genomes that we term Phylogenetically-Informed Annotation (PIA), which places uncharacterized genes into pre-calculated phylogenies of gene families. Results: We generated maximum likelihood trees for 109 genes from a Light Interaction Toolkit (LIT), a collection of genes that underlie the function or development of light-interacting structures in metazoans. To do so, we searched protein sequences predicted from 29 fully-sequenced genomes and built trees using tools for phylogenetic analysis in the Osiris package of Galaxy (an open-source workflow management system). Next, to rapidly annotate transcriptomes from organisms that lack sequenced genomes, we repurposed a maximum likelihood-based Evolutionary Placement Algorithm (implemented in RAxML) to place sequences of potential LIT genes on to our pre-calculated gene trees. Finally, we implemented PIA in Galaxy and used it to search for LIT genes in 28 newly-sequenced transcriptomes from the light-interacting tissues of a range of cephalopod mollusks, arthropods, and cubozoan cnidarians. Our new trees for LIT genes are available on the Bitbucket public repository (http://bitbucket.org/osiris_phylogenetics/pia/) and we demonstrate PIA on a publicly-accessible web server (http://galaxy-dev.cnsi.ucsb.edu/pia/). Conclusions: Our new trees for LIT genes will be a valuable resource for researchers studying the evolution of eyes or other light-interacting structures. We also introduce PIA, a high throughput method for using phylogenetic relationships to identify LIT genes in transcriptomes from non-model organisms. With simple modifications, our methods may be used to search for different sets of genes or to annotate data sets from taxa outside of Metazoa