Isolation of DNA sequences with homology to a degenerate FaRP oligonucleotide from the crayfish Procambarus clarkii

The neuropeptide Th1RFamide with the sequence Phe-Met-Arg-Phe-amide was originally isolated in the clam Macrocallista nimbosa (price and Greenberg, 1977). Since its discovery, a large family ofFl\1RFamide-related peptides termed FaRPs have been found to be present in all major animal phyla with functions ranging from modulation of neuronal activity to alteration of muscular contractions. However, little is known about the genetics encoding these peptides, especially in invertebrates. As FaRP-encoding genes have yet to be investigated in the invertebrate Malacostracean subphylum, the isolation and characterization ofFaRP-encoding DNA and mRNA was pursued in this project. The immediate aims of this thesis were: (1) to amplify mRNA sequences of Procambarus clarkii using a degenerate oligonucleotide primer deduced from the common amino acid sequence ofisolated Procambarus FaRPS, (2) to determine if these amplification products encode FaRP gene sequences, and (3) to create a selective cDNA library of sequences recognized by the degenerate oligonucleotide primer. The polymerase chain reaction - rapid amplification of cDNA ends (PCR-RACE) is a procedure in which a single gene-specific primer is used in conjunction with a generalized 3' or 5' primer to amplify copies ofthe region between a single point in the transcript and the 3' or 5' end of cDNA of interest (Frohman et aI., 1988). PCRRACE reactions were optimized with respect to primers used, buffer composition, cycle number, nature ofgenetic substrate to be amplified, annealing, extension and denaturation temperatures and times, and use of reamplification procedures. Amplification products were cloned into plasmid vectors and recombinant products were isolated, as were the recombinant plaques formed in the selective cDNA library. Labeled amplification products were hybridized to recombinant bacteriophage to determine ligated amplification product presence. When sequenced, the five isolated PCR-RACE amplification products were determined not to possess FaRP-encoding sequences. The 200bp, 450bp, and 1500bp sequences showed homology to the Caenorhabditis elegans cosmid K09A11, which encodes for cytochrome P450; transfer-RNA; transposase; and tRNA-Tyr, while the 500bp and 750bp sequences showed homology with the complete genome of the Vaccinia virus. Under the employed amplification conditions the degenerate oligonucleotide primer was observed to bind to and to amplify sequences with either 9 or 10bp of 17bp identity. The selective cDNA library was obselVed to be of extremely low titre. When library titre was increased, white. plaques were isolated. Amplification analysis of eight isolated Agt11 sequences from these plaques indicated an absence of an insertion sequence. The degenerate 17 base oligonucleotide primer synthesized from the common amino acid sequence ofisolated Procambarus FaRPs was thus determined to be non-specific in its binding under the conditions required for its use, and to be insufficient for the isolation and identification ofFaRP-encoding sequences. A more specific primer oflonger sequence, lower degeneracy, and higher melting temperature (TJ is recommended for further investigation into the FaRP-encoding genes of Procambarlls clarkii.

An exploratory study for the discovery of non-invasive hepatocellular carcinoma biomarkers among high-risk hepatitis C virus infected patients

Hepatocellular Carcinoma (HCC) is a major healthcare problem, representing the third most common cause of cancer-related mortality worldwide. Chronic infections with Hepatitis B virus (HBV) and/or Hepatitis C virus (HCV) are the major risk factors for the development of HCC. The incidence of HBV -associated HCC is in decline as a result of an effective HBV vaccine; however, since an equally effective HCV vaccine has not yet been developed, there are 130 million HCV infected patients worldwide who are at a high-risk for developing HCC. Because reliable parameters and/or tools for the early detection of HCC among high-risk individuals are severely lacking, HCC patients are always diagnosed at a late stage where surgical solutions or effective treatment are not possible. Using urine as a non-invasive sample source, two different approaches (proteomic-based and genomic-based approaches) were pursued with the common goal of discovering potential biomarker candidates for the early detection of HCC among high-risk chronic HCV infected patients. Urine was collected from 106 HCV infected Egyptian patients, 32 of whom had already developed HCC and 74 patients who were diagnosed as HCC-free at the time of initial sample collection. In addition to these patients, urine samples were also collected from 12 healthy control individuals. Total urinary proteins, Trans-renal nucleic acid (Tr-NA) and microRNA (miRNA) were isolated from urine using novel methodologies and silicon carbide-loaded spin columns. In the first, "proteomic-based", approach, liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) was used to identify potential candidates from pooled urine samples. This was followed by validating relative expression levels of proteins present in urine among all the patients using quantitative real time-PCR (qRT-PCR). This approach revealed that significant over-expression of three proteins: DJ-1, Chromatin Assembly Factor-1 (CAF-1) and 11 Moemen Abdalla HCC Biomarkers Heat Shock Protein 60 (HSP60), were characteristic events among HCC-post HCV infected patients. As a single-based HCC biomarker, CAF-1 over-expression identified HCC among HCV infected patients with a specificity of 90%, sensitivity of 66% and with an overall diagnostic accuracy of 78%. Moreover, the CAF-lIHSP60 tandem identified HCC among HCV infected patients with a specificity of 92%, sensitivity of 61 % and with an overall diagnostic accuracy of 77%. In the second genomic-based approach, two different approaches were processed. The first approach was the miRNA-based approach. The expression levels of miRNAs isolated from urine were studied using the Illumina MicroRNA Expression Profiling Assay. This was followed by qRT-PCR-based validation of deregulated expression of identified miRNA candidates among all the patients. This approach shed the light on the deregulated expression of a number of miRNAs, which may have a role in either the development of HCC among HCV infected patients (i.e. miR-640, miR-765, miR-200a, miR-521 and miR-520) or may allow for a better understanding of the viral-host interaction (miR-152, miR-486, miR-219, miR452, miR-425, miR-154 and miR-31). Moreover, the deregulated expression of both miR-618 and miR-650 appeared to be a common event among HCC-post HCV infected patients. The results of the search for putative targets of these two miRNA suggested that miR-618 may be a potent oncogene, as it targets the tumor-suppressor gene Low density lipoprotein-related protein 12 (LPR12), while miR-650 may be a potent tumor-suppressor gene, as it is supposed to downregulate the TNF receptor-associated factor-4 (TRAF4) oncogene. The specificity of miR-618 and miR-650 deregulated expression patterns for the early detection of HCC among HCV infected patients was 68% and 58%, respectively, whereas the sensitivity was 64% and 72%, respectively. When the deregulated expression of both miRNAs was combined as a tandem biomarker, the specificity and the sensitivity were 75% and 58% respectively. 111 Moemen Abdalla HCC Biomarkers In the second, "Trans-renal nucleic acid-based", approach, the urinary apoptotic nucleic acid (uaNA) levels of 70ng/mL or more were found to be a good predictor of HCC among chronic HCV infected patients. The specificity and the sensitivity of this diagnostic approach were 76% and 86%, respectively, with an overall diagnostic value of 81 %. The uaNA levels positively correlated to HCC disease progression as monitored by epigenetic changes of a panel of eight tumor-suppressor genes (TSGs) using methylation-sensitive PCR. Moreover, the pairing of high uaNA levels (:::: 70 ng/mL) and CAF-1 over-expreSSIOn produced a highly specific (l 00%) multiple-based HCC biomarker with an acceptable sensitivity of 64%, and with a diagnostic accuracy of 82%. In comparison to the previous pairing, the uaNA levels (:::: 70 ng/mL) in tandem with HSP60 over-expression was less specific (89%) but highly sensitive (72%), resulting in a diagnostic accuracy of 64%. The specificities of miR-650 deregulated expression in combination with either high uaNA content or HSP 60 over-expression were 82% and 79%, respectively, whereas, the sensitivities of these combinations were 64% and 58%, respectively. The potential biomarkers identified in this study compare favorably with the diagnostic accuracy of the a-fetoprotein levels test, which has a specificity of 75%, sensitivity of 68% and an overall diagnostic accuracy of 70%. Here we present an intriguing study which shows the significance of using urine as a noninvasive sample source for the identification of promising HCC biomarkers. We have also introduced new techniques for the isolation of different urinary macromolecules, especially miRNA, from urine. Furthermore, we strongly recommend the potential biomarkers indentified in this study as focal points of any future research on HCC diagnosis. A larger testing pool will determine if their use is practical for mass population screening. This explorative study identified potential targets that merit further investigation for the development of diagnostically accurate biomarkers isolated from 1-2 mL urine samples that were acquired in a non-invasive manner.

Benjamin Woodruff Price Papers, 1851, 1853-1860, 1862-1863, 1874, n.d.

The fonds includes sixty two items of correspondence between Benjamin Woodruff Price, aka Woodruff, Ben or Uncle, and various family members, both immediate and distant cousins. Also included is business correspondence related to Price’s activities as a watchmaker and/or jeweler. Benjamin Woodruff Price was born in Thorold Township ca. 1831, the son of Joseph Price and Mary Smith. B.W. Price married Ella or Ellen McGlashan (1851-1906) ca. 1868. Price died between 1891 and 1901, his burial location is unknown at present. A watchmaker and jeweler, Price lived most of his life in Fonthill, Ont. He also included auctioneer, undertaker and photographer as some of his other professional activities. His siblings included David Smith Price (wife Isabella Ann), John Smith Price (wife Elizabeth Jane), and sisters Susan Page (husband Edward Rice Page), Jerusha Price, Mary Price and Martha W. Stone (husband Dudley Ward Stone). John Smith Price died 18 April 1860, leaving no descendents. It is likely that G.W. Stone was a nephew to B.W. Price, the son of his sister Martha W. Stone and her husband Dudley Ward Stone. Susan Page was a sister of Benjamin Woodruff Price. She was married to Edward Rice Page and they had at least two children, Joseph and Clayton. At the time of this correspondence they lived in Suspension Bridge, NY, now part of Niagara Falls, New York. Edward Rice Page’s occupation was listed as saloon keeper. The Price family appears to have had a very large extended family. This information was gleaned from the contents of letters of Maggie Tisdale, daughter of Ephraim and Hannah (Price) Tisdale, P.A. or Ann Morgan, [may also be Phebe Ann] of Newark, NY? and Marietta House of Bayham Township. DeWitt Higgins of Suspension Bridge, NY aka Niagara Falls, NY was an auctioneer, specialized in buying jewellery, watches, clocks, from individuals and reselling his product to others like B.W. Price.

Welland Canal Survey of Lands David Price, 1834

Survey map and description of David Price's land created by The Welland Canal Company. Included is a written description of the land along with a drawing of the land. Noteable features include; Hellem's Creek, road, bridge, Chippewa, Griffith's land, canal. The deed for the land is dated October 14, 1834. The land totals 5 acres, 3 roads and 7 perches. Surveyor notes are seen in pencil and red pen on the map.

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.

The Impact of a Corporate Name Change on Stock Price and Trading Volume of Canadian Companies

This thesis examines the impact of a corporate name change on stock price and trading volume of Canadian companies around the announcement date, the approval date, and the adoption date over the time period from 1997 to 2011. Name changes are classified into six categories: major and minor, structural and pure, diversified and focused, accompanied with a change in ticker symbol and without a change in ticker symbol, “Gold” name addition and deletion, and different reasons for name changes (e.g., merger and acquisition, change of structure, change of strategy, and better image). The thesis uses the standard event study methodology to perform abnormal return and trading volume analyses. In addition, regression analysis is employed to examine which type of a name change has the largest impact on cumulative abnormal returns. Sample stocks exhibit a significant positive abnormal return one-day prior to the approval day and one day after the adoption date. Around the approval date we observe significant abnormal returns for stocks with a structural name change. On the day after the adoption date we document abnormal returns for stocks with major, minor, structural, pure, focused, and ticker symbol name changes. If a merger or acquisition is the reason for a name change, companies tend to experience a significant positive abnormal return one-day before the approval date and on the adoption date. If a change of structure is the reason for a name change, companies exhibit a significant positive abnormal return on the approval date and a significant negative abnormal return on the adoption date. In case of a change of strategy as the reason for a name change, companies show a significant negative abnormal return around the approval date and a significant positive abnormal return around the adoption date.

Alberta Price List No. 3., January 1st, 1925

A price list form for the Alberta Liquor Control Board from 1 January 1925. The price list includes "General Information" in regards to permits for individuals and special permits. The alcohol is then listed by category for pricing: Scotch Whisky, Irish Whisky, Rye Whisky, Bourbon Whisky, Rum, Gin, Brandy, Port, Native Wine, Italian (Type) Wines, Sherry, Claret, Burgundy, White Wine, Sparkling Wine, Vermouth, Cocktails, Liqueurs, Champagne, Bitters, Ale and Stout, Chinese Liquors.

General Price List, Ontario, 1 January 1924

A general price list from the year 1924 for the province of Ontario. The cover of the list reads: "Ontario Government Dispensaries Conducted Under Direction of Board of License Commissioners for Ontario By Authority of The Ontario Temperance Act. General Price List, Dispensaries sell liquor for medicinal, sacramental, scientific and manufacturing purposes only. The sale of liquor for beverage purposes in the Province of Ontario is prohibited by The Ontario Temperance Act. Dispensaries: No.1-154 Wellington Street West, Toronto; No.2-1271 Dundas Street West, Toronto; No.3-29 Charles Street, Hamilton; No.4-425 Talbot Street, London; No.5-30 Sandwich Street West, Windsor; No.6-Golden Lion Block, Kingston; No.7-92 Kent Street, Ottawa; No.8-109 Simpson Street, Fort William."

Newfoundland Price List, 1 June 1928

A price list for Newfoundland by the Board of Liquor Control, St. John's. The list is one page in length and has a few handwritten changes to prices.

Price List - Lawrence A. Wilson Co. Limited, 1916

A price list for Lawrence A. Wilson Co. Limited, 87 James St., Montreal Quebec. It is addressed to The Toronto Hunt, 52 Bay Street, Toronto. There are additional handwritten notes. One of the handwritten notes reads "ck to W. Stephen Haas"

Wiehl & Widmann Price List, August 1903

A price list for Wiehl & Widmann (Wholesale Importers of and Dealers in Wines, Liquors and Mineral Waters). The price list is dated August 1903 and the location of the dealer is New York.

The "Bodega" Company Price List

A price list for The "Bodega" Company Limited. The company has branches throughout the United Kingdom, including: London, Birmingham, Manchester, Liverpool, Glasgow, Edinburgh, Dundee, Brighton, and Ryde. The final pages of the price list also include a reprinted article from "The Irish Times" concerning a case against the use of the Bodega Company name.

Artists Rendering of Isobel Price

Artist’s rendering in colour of Isobel Price in an oval frame with a hook at the top and a section at the back which contains a lock of hair. This painting was done by Gerald Sinclair Hayward who was a renowned artist whose work was displayed at an exhibition in New York in 1899. He painted Theodore Roosevelt, William K. Vanderbilt and members of the ruling families of Britain, Germany and Russia. The frame is enclosed in a folding case lined with velvet and silk. The silk is quite worn. The outside of the case appears to be leather and has a stand for setting it upright. It closes with a metal latch. This is accompanied by a note by R. Band.

Indenture between Samuel Street and Eunice Price

Indenture (vellum) of bargain and sale between Samuel Street of Stamford and Eunice Price widow of the late David Price of Willoughby regarding a part of Lot no. 15 in the 5th Concession in Humberstone - instrument no. 1141, June 14, 1842.

Letter to Isabel from Phil [Phil Ingram Price]

Letter to Isabel from Phil [Phil Ingram Price] in which he expresses a desire to divide the estate with as little delay as possible. He has divided the books into 4 lots, but he asks if Isabel has some of the books as they are missing, March 28, 1900.