A Multi-Objective Genetic Algorithm with Side Effect Machines for Motif Discovery

Understanding the machinery of gene regulation to control gene expression has been one of the main focuses of bioinformaticians for years. We use a multi-objective genetic algorithm to evolve a specialized version of side effect machines for degenerate motif discovery. We compare some suggested objectives for the motifs they find, test different multi-objective scoring schemes and probabilistic models for the background sequence models and report our results on a synthetic dataset and some biological benchmarking suites. We conclude with a comparison of our algorithm with some widely used motif discovery algorithms in the literature and suggest future directions for research in this area.

Bringing Zombies Back to Life: An Autoethnographical Exploration of Alienation and Political Dis/Engagement in Emerging Adulthood Within Late-Stage Capitalism

In this thesis, by employing an autoethnographic methodology, I am exploring why certain understandings, or assemblages, of political engagement come to have greater meaning in my life and why other assemblages may be more hidden and thus fail to contribute substantially to the meaning of political in my life. Using immanent, Marxist and post-Marxist theories, as well as a zombie narrative, the study will contextualize the movement of assemblages in my life within late-stage capitalism which is juxtaposed with the zombie apocalypse. The placement and displacement of certain understandings of the political within my life will be theorized within the crisis of constituent power that is revealed in an immanent framework. Furthermore, the crisis of the constituent in late-stage capitalism creates new forms of radical alienation which will also be examined. By exploring my own struggles in becoming political I will theorize why political disengagement in emerging adulthood appears to be increasing, as well as possibilities for new forms of political engagement in a late-stage capitalist context.

Message from the President of the United States transmitting documents relative to the execution of the first article of the late treaty between the United States and Great Britain.

"February 7, 1817, ordered to be printed for the use of the Senate." Message addressed to the Senate and dated February 7th, 1817. Consists of the covering letter from the President and a report from the Secretary of State, dated Department of State, February 5th, 1817; which itself consists largely of diplomatic correspondence between the United States and Great Britain Relates to the restitution of captured slaves by the British during the War of 1812-1814.

The γ-tocopherol-like family of N-methyltransferases: A taxonomically clustered gene family encoding enzymes responsible for N-methylation of monoterpene indole alkaloids

The plant family Apocynaceae accumulates thousands of monoterpene indole alkaloids (MIAs) which originate, biosynthetically, from the common secoiridoid intermediate, strictosidine, that is formed from the condensation of tryptophan and secologanin molecules. MIAs demonstrate remarkable structural diversity and have pharmaceutically valuable biological activities. For example; a subunit of the potent anti-neoplastic molecules vincristine and vinblastine is the aspidosperma alkaloid, vindoline. Vindoline accumulates to trace levels under natural conditions. Research programs have determined that there is significant developmental and light regulation involved in the biosynthesis of this MIA. Furthermore, the biosynthetic pathway leading to vindoline is split among at least five independent cell types. Little is known of how intermediates are shuttled between these cell types. The late stage events in vindoline biosynthesis involve six enzymatic steps from tabersonine. The fourth biochemical step, in this pathway, is an indole N-methylation performed by a recently identified N-methyltransfearse (NMT). For almost twenty years the gene encoding this NMT had eluded discovery; however, in 2010 Liscombe et al. reported the identification of a γ-tocopherol C-methyltransferase homologue capable of indole N-methylating 2,3-dihydrotabersonine and Virus Induced Gene Silencing (VIGS) suppression of the messenger has since proven its involvement in vindoline biosynthesis. Recent large scale sequencing initiatives, performed on non-model medicinal plant transcriptomes, has permitted identification of candidate genes, presumably involved, in MIA biosynthesis never seen before in plant specialized metabolism research. Probing the transcriptome assemblies of Catharanthus roseus (L.)G.Don, Vinca minor L., Rauwolfia serpentine (L.)Benth ex Kurz, Tabernaemontana elegans, and Amsonia hubrichtii, with the nucleotide sequence of the N-methyltransferase involved in vindoline biosynthesis, revealed eight new homologous methyltransferases. This thesis describes the identification, molecular cloning, recombinant expression and biochemical characterization of two picrinine NMTs, one from V. minor and one from R. serpentina, a perivine NMT from C. roseus, and an ajmaline NMT from R. serpentina. While these TLMTs were expressed and functional in planta, they were active at relatively low levels and their N-methylated alkaloid products were not apparent our from alkaloid isolates of the plants. It appears that, for the most part, these TLMTs, participate in apparently silent biochemical pathways, awaiting the appropriate developmental and environmental cues for activity.

Notice of sale regarding the late Ezekiel Cudney’s property including the dwelling, barn and fruit trees

Notice of sale regarding the late Ezekiel Cudney’s property including the dwelling, barn and fruit trees. The land contains 39 acres of parts of Lots 9 and 10 on the Welland River in the Township of Willoughby. The notice states that you must apply to S.D. Woodruff of St. Catharines. This is handwritten on a small piece of paper, Dec. 5, 1892.

Receipt to the Estate of the late J.A. Woodruff from Dr. John Comfort

Receipt to the Estate of the late J.A. Woodruff from Dr. John Comfort for medical services, Oct. 5, 1886.

Receipt to the Estate of the late J.A. Woodruff from McIntyre and Son, Professional Embalmers and Undertakers and Funeral Directors

Receipt to the Estate of the late J.A. Woodruff from McIntyre and Son, Professional Embalmers and Undertakers and Funeral Directors, St. Catharines for funeral services, Oct. 14, 1886.

Indenture between the Honourable William Dickson of Dumphries, trustee and executor for the late Honourable Robert Hamilton Dickson to Samuel Street of Stamford

Indenture between the Honourable William Dickson of Dumphries, trustee and executor for the late Honourable Robert Hamilton Dickson to Samuel Street of Stamford for 50 acres in the Township of Gainsboro consisting of part of no. 27 in the 2nd Concession – instrument no. 599, Dec. 30, 1841.

History of the Late War between Great Britain and the United States of America

History of the Late War between Great Britain and the United States of America by David Thompson, late of the Royal Scots, Niagara U.C. , 1832. There is an inscription in the front of the book which says “[illegible] Nelles, Grimsby and it is signed by Joseph Williams [?]” The book is stained from dampness, but this does not affect the text, 1832.