1,460 research outputs found
An overview of the wcd EST clustering tool
No full textHazelhurst S, Hide W, Lipták Z, Nogueira R, Starfield R. An overview of the wcd EST clustering tool. BIOINFORMATICS. 2008;24(13):1542-1546.The wcd system is an open source tool for clustering expressed sequence tags (EST) and other DNA and RNA sequences. wcd allows efficient all-versus-all comparison of ESTs using either the d(2) distance function or edit distance, improving existing implementations of d(2). It supports merging, refinement and reclustering of clusters. It is drop in compatible with the StackPack clustering package. wcd supports parallelization under both shared memory and cluster architectures. It is distributed with an EMBOSS wrapper allowing wcd to be installed as part of an EMBOSS installation (and so provided by a web server)
Author Arna Bontemps reads to children at the East Winston Branch Library, 1956.
No full textAuthor Arna Bontemps reads to children at the East Winston Branch Library, 1956
Urban heat island research in Phoenix, Arizona: Theoretical contributions and policy applications
No full textabstract: This review investigates the possible reasons and motivations underpinning the large body of work, as well as summarizing specific themes, approaches, and theoretical contributions arising from such study.Corresponding Author:
Winston T. L. Chow
Arizona State University
[email protected]
Winston Churchill High School The Statesman 1961
No full textThe annual publication of the students of Winston Churchill High School, Lethbridge, Alberta. (Volume I. 1960-61)pdfThe States mon
Satisfaction Through Qchieve[tient
Qnnua! Pub!/cation of the Students of lOinstorr Churchill High School jCethbridye, Siberia
VOLUME I 1960-61IVK'O^40^
You are young, my son, and as the years go by, time will change and even reverse many of your present opinions. Refrain therefore awhile from setting yourself up as a judge of the highest matters.
— Plato
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Dedication
This first volume of The Statesman
is respectfully dedicated to the memory of the late A. J. Watson
The Students of Churchill School _ owe A. J. Watson a debt of
gratitude for his untiring efforts in the development of this school as well as his contribution to education generally.
His work on behalf of the students of this city will long be remembered.
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Introduction
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Dedication
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In Memorium
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Principal’s Message
Student Council Statesman Staff
Faculty
Churchill Chatter Staff
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Parent's Association Executive
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Student Pictures Grade XI
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Grade X
1AND?A DOUGHTY. STAN FURAKAWA. WHURO ROUOFS. KIKU KlTAGAY/A. JIM MAXWGlL, GAIL SEA6EP GAIL THOMPSON.
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BACK ROW- 0 COOPER (J-W. V.p) MRS E-WAllDEW. (TREASURER), MRS. M. Slfc'GURDSON. MRS. MATHESON. MRS. o. ASPLOMO. MR. McCOtNAN (viO£ Pfc£SjD£>Jrj
FRONT" R.0W - MRS. J. PlERCHALA (SOC/AL dOMV£NEft\ MRS MoBEfc. MRS. J. N£ELY (SECRETARY) M«i. J- WALK6H (PR£&»0£nt)i MRS. U. WAUCGR (PROGRAM CONVEMCP), MRS MO«ft'*OM
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BARNETT, Sharon - Room 101- Captain of Cheerleaders BAUER, Sharon - Room 105 BLOCK, Clifford - Room 101
BOC-USKY, Donna - Room 101 BROWN, Gayle - Room 101 BRUCE, Pat - Room 105
CHOLLACK, Richard - Room 101 CHOMICKI, John - Room 105 .COOPER, Lynda - Room 101
DOROK, Tillie - Room 105 DUFF, Lynn - Room 101 EVDOKIMOFF, Wally - Room 101- Room Representative
FORD, Wilfred - Room 105 FRANK, Carol - Room 105 FRIEND, Mickey - Room 101
FRITZ, Elfriede - Room 105 GODSALVE, Rosanne - Room 105 GRISAK, Sharron - Room 105- Treasurer of Student Council
GUENTHER, Velma - Room 101 HANDLEY, Bev - Room 105 HEGLAND, Harold - Room 105- Room Representative
HEGLAND, Judy - Room 101 HELWIG, Dick - Room 105- President of Booster Club HEWER, Janet - Room 105
JACKSON, Jackie - Room 101 JOHNSTON, Alex - Room 105 KESLER, Pat - Room 105
KINNELL, Leslie - Room 101 KOCH, Leon - Room 101 KOSAKA, Thelma - Room 105- President of Student Council
KOZAK, Katie - Room 105- Secretary of Student Council LAING, Cameron - Room 105 LEE, Victor - Room 105
LEITCH, Ken - Room 101 LORENCZ, Floyd - Room 101 LOWE, Frances - Room 105
MATT, Ed - Room 101 McADAM, Maureen - Room 105 NORLIN, Trevor - Room 105
ONOFRYCHUK, Mike - Room 105 POHL, Volkmar - Room 105 PONECH, Joanne - Room 101
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QUANDT, Irene - Room 101- Secretary of Girl's Choir REID, Bryan - Room 10
RYLL, Irma - Room 10 SMEED, Sharon - Room 101
STEDMAN, Derek - Room 101 THOMPSON, Gail - Room 101 TOLLESTRUP, Barry - Room 101
rOMASKI, Sharon - Room 101 TROCKSTAD, Bruce - Room 101 TUTTLE, Frank - Room 101
VALKENIER, Peter - Room 10 WALKER, Leslie - Room 10 WOHLGEMUTH, Don - Room 101 WOOLDRIDGE, Faye - Room 10
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ALLEN, Don - Room 106 BAGOZZI, Don - Room 10Li BAKER, Gail - Room iOh
FURUKAWA, Stanley - Room IOh GANGUR, Jerry - Room iOli Room Representative GAST, Art - Room 110
BODELL, Dale - Room 110 BRADY, Allen - Room 106 BRADY, Doreen - Room 106
GRAY, Don - Room 106 GREEN, David - Room 110 GR0TT0L0, Dennis - Room 106
CARLETON, Ivor - Room 110 CHAPMAN, Bob - Room 110 CHAPMAN, Rae - Room 106
HALL, Robert - Room 10U President of Electronics Club HANSEN, Edith - Room 106 HCWELL, Ken - Room 106
CHEESMAN, Judy - Room IOh CHRISTIE, Bob - Room 110 CHRISTIE, Pat - Room 106
HOSTLAND, Kathy - Room 106- Vice-President of Student Council HRA8IC, Judy - Room 106 HUBER, Donna - Room 108
CLOSE, Guy - Room 106- Room Representative COUTTS, Carole - Room 108 COUTTS, Ricky - Room 1C6
HUGHES, Carole - Room 108 JARVIE, Vernon - Room 110 JOHNSON, Sandra - Room 108
DAW, Art - Room 110
DES HOSIERS, Judy - Room 106
DORCHAK, Frank - Room 106
KAZAKOFF, John - Room 106 KETHLER, Ken - Room 106 KITAGAWA, Kiku - Room 10U- Editor of School Paper
DOUGHTY, Sandra - Room 108- Room Representative ERICKSON, Bob - Room 110 FRITZLER, Donna - Room 108
KITAGAWA, Terry - Room IOh KLAUS, Sharon - Room 108 KLIMOW, Sina - Room 10U
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LANGHOFER, Dwight - Room 106 LEMKE, Art - Room 106 LILLENIIT, Juri - Room lOh
PETROVICH, Marion - Room 108 POCH, Ron - Room 110 PONECH, Ron - Room lOlj
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LOXTON, Mickey - Room 106 MALLETT, Georgeina - Room IOh MANNING, Fred - Room 110
PYSH, Dave - Room 110 QUINELL, Pat - Room 108 RADLEY, Mary-Anne - Room IOh
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MASSON, Linda - Room 103 MATHESON, Dwayne - Room 106 MATTHEWS, Bryan - Room 110
REEDYK, Martin - Room 10U- President of Chess Club REIDEL, Bill - Room 110 RENTER, Karl - Room 110
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MAXWELL, Jim - Room 10L McMILLAN, Stuart - Room 106 MOODIE, Dennis - Room 106
ROELOFS, Brian - Room 106 ROELOFS, William - Room 10U ROGERS, Gloria - Room 106
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MORITA, Darlene - Room 106 MORRISON, Rod - Room 10h MURAKAMI, Doreen - Room 10h
RUNQUIST, Don - Room IOh SEAGER, Gail - Room 103 SETOGUCHI, Bob - Room IOh
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MURAKAMI, Maxine - Room 10h NEELY, Mary - Room iOU- Editor of Yeai*book NESS, Lome - Room 10L
SHAW, Louise - Room 106 SHIMOZAWA, Diane - Room 108 SIMMONS, Dale - Room 106
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NETTLETON, Sharon - Room 108- Secretary of Bowling Club PETERS, Ruth - Room iOh PETRIE, Ricky - Room 110
SINCLAIR, John - Room 110 SLAWSON, Karen - Room 103 SLOBODIAN, Bob - Room 106
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STEDMAN, Janet - Room 10U TAYLOR , 3ev - Room 108 TKACHENKO, Nick - Room 110- Room Representative
TYZNENKO, Luba - Room lOh VANDER MOLEN, Elizabeth - Room 108 VAN WEELE, Cornelius - Room 10L
WALLDEN, Ivie - Room 10U WATSON, Walter - Room lOh- Secretary of Chess Club WICKERSHAM, Tom - Room 106
WILKIE, Alan - Room 110 WOODCOCK, Christine - Room 106 WOHLEGEMUTH, Judy - Room 106
YAMAGISHI, Irene - Room 106
CUSTODIAL STAFF
J. Green J. Smith C. Sherring R. Anderson
Mrs. M. Soltys Mrs. L. Huber Mrs. Parsons
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ALLEN, Dennis - Room 206- Room Representative ALLEN, Tom - Room 208 ASPLUND, Warren - Room 208
BAG022I, Robert - Room 2C6 BAGU, Shirley - Room 201* BAINS, Dixie - Room 202
BARNABY, Jerry - Room 210 BARTLETT, Pat - Room 202- Room Representative BARTON, Glen - Room 206
BARVA, Alan - Room 208 BEALL, Leslie - Room 202 BLACK, Roger - Room 208
BLOCK, La Verne - Room 210 BLOCK, Sandra - Room 20L BODELL, Sharon - Room 20li
BOEHR, Doug - Room 2C6 BOSCH, Henry - Room 2C6 BOUTESTEIN, Bill - Room 208
BRADY, Ron - Room 210 BRASSARD, Gladys - Room 202 BROWN, Mike - Room 210
BROWN, Ron - Room 210 CHECKLEY, Don - Room 206 CHUDOBIAK, Bill - Room 210
CHUMIK, Glenys - Room 202 COOK, Ken - Room 208 COUTTS, John - Room 206
CCUTTS, Sharon - Room 202 COYLE, Pat - Room 20h CRABB, Diana - Room 202
CUTLER, Jim - Room 206 DE JAGER, Hilda - Room 202 DOUGHTY, Carol - Room 20L
DOUGLAS, Roy - Room 208 DUFF, Frank - Room 210- Room Representative EMERY, Heather - Room 202
ENANDER, Ken - Room 206 FIRTH, Maxine - Room 201* FLEMING, Jack - Room 208
FLETCHER, June - Room 202 F0RD,< Fred - Room 208 FRANK, Joe - Room 206
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FRASER, Delores - Room 202 GREEN, Peter - Room 206 GREENE, Earl - Room 208'
GODSALVE, Maureen - Room 202 HACKER, Tom - Room 210 HAGGITT, Knox - Room 210
HANDLEY, Dick - Room 208 HERSFT, Alice - Room 202 HILL, Bev - Room 20h
HOFMAN, Elsie - Room 20L HOUGHTON, Pat - Room 20h HOWARD, Doug - Room 206
HOWARD, Rochelle - Room 20L HOWELL, Lanny - Room 206 INGOLDSBY, Cheryl - Room 202
JACOBSON, June - Room 202 JARVIS, Bev - Room 202 JORDAN, Gwen - Room 20L
KANE, John - Room 208 KAZAKOFF, Paul - Room 206 KEARNEY, Kathy - Room 202
KERR, Doreen - Room 20U KETCHESON, Dale - Room 210 KOK, Sidney - Room 208
KOLESZAR, Priscilla - Room 20h KRUCHKYWICH, John - Room 210 LAMB, Garth - Room 206
LARSEN, Eleanor - Room 20U LEE, Don - Room 208 LEE, Ivy - Room 202
LEISHMAN, Denise - Room 20U LIGHTIZER, Gail - Room 20h LOULA, Clara - Room 202
LOUWERSE, Henry - Room 210 MANNING, Valerie - Room 20h MARTIN, Doug - Room 206
MARTIN, Pat - Room 202 MARUS, Elizabeth - Room 20h McADAM, Roger - Room 206
McCAGHERTY, Wayne - Room 208 McCOLLUM, Dennis - Room 208 McCUAIG, Dick - Room 208
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McCUAIG, Judy - Room 20h McCOWAN, Gordon - Room 208 McMURREN, Roy - Room 206
MERCER, Barbara - Room 20h MOKOSKI, Marion - Room 20U MORRISON, Buzz - Room 206
'ESS, Dennis - Room 210 OAKES, Alexander - Room 210 OHAMA, Ron - Room 206
OHNO, Carol - Room 202- Grade 9 Treasurer OKITA, Lloyd - Room 206 ONOFRYCHUK, Barrie - Room 206
ORICK, Eugene - Room 208 OSLANSKY, Bob - Room 210 PARKINSON, Richard - Room 208
PERDUE, Jean - Room 20h PICKLES, Reg - Room 208 PIER2CHALA, Gail - Room 202
PONECH, Tom - Room 208 POULSON, Monty - Room 208 PYSH, Joe - Room 206
QUIIELL, Josephine - Room 20U RADICS, Julie - Room 202 REIERSOJJ, Kermit - Room 208
ROBULAK, Linda - Room 20L ROELOFS, Morley - Room 210 RCWLEY, Dave - Room 210
RUD, Byron - Room 208 RUSLING, Wayne - Room 206 SQiALK, Peter - Room 208
SELVIG, Janice - Room 20U SHAIL, Dawn - Room 20h SHANKS, George - Room 210
SIGURDSON, Dave - Room 208 SMID, Douwe - Room 206 S0L0WJ0W, Stella - Room 20h
STEVENSON, Margaret - Room 20h- Room Representative TAPPER, Janet - Room 202 TKACHENKO, Lily - Room 202
TOIVANEN, Terry - Room 208 TRENTINI, Dale - Room 210 TUTJOW, Margaret - Room 20L
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URBAN, Marlene - Room 20li URBAN, Vera - Room 20U VAN WEELE, Thys - Room 210
VASELENAK, Jeanette - Room 202 VIBERT, Phil - Room 203 VIETORISZ, Dennis - Room 206
VOORT, Tony - Room 208 WALKER, Edward - Room 210 WALKER, Leroy - Room 206
WEBER, Horst - Room 206 WEIKEL, Doug - Room 206 WILLIS, Allen - Room 210
WILLIS, Edna - Room 202 WILSON, Robert,- Room 210 WOODS, Tom - Room 210
WYROSTOCK, Don - Room 210 YAMAGISHI, Don - Room 208- Room Representative SHIGEHERO, Peggy - Room 202
Hard work is the accumulation of easy things that you did not do when you should have.
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It is indeed an honor and a privilege to present this address. The significance of this evening will long be remembered as an important event in the course of our lives, for it represents the completion of nine years of study, recreation and companionship.
As we look back over the years, we may smile, as we think of the problems and experiences which confronted us. They may have seemed unconquerable at the time, however, as author Arthur Guitermann implies, "Time changes all things." Therefore, what seemed unsurmountable then, is now, a mere recollection of the past.
We may recall the days when we entered school for the first time. We were cast into a new world of pencils, books and more books. It was also here that we experienced the disciplinary action of the teachers, finding them somewhat similar to that of our parents. It was in this "Ace of Innocence", that small problems seemed overwhelmingly difficult and we often wondered if ever, we would grow up. Thus a period of six years came to an end.
We were, perhaps, sad in our farewell to elementary school and in leaving comfortable habits. This only presented temporary worries, however, for the prospect of attending a larger school, meeting new friends and acquiring greater knowledge, remained constantly in our minds.
This oeriod has now come to a close and we must look to the future in the anticipation of attaining new heights and in overcoming the difficulties which may arise.
Now, as we look around this hall, seeing all these happy and proud faces, it leaves us with sadness, knowing that some of us will not be here in. the future. This is softened somewhat, since each of us has a worthwhile purpose to fulfill in life.
We must also consider and be thankful for the love and affection of our parents and the constant guidance of the teachers, who, in their efforts helped us to further our schooling.
Thus, it is in this state of mind that I wish to congratulate you, and wish you all the "best in the years to come. Let us all be prepared to use what we have gained to make this world of ours a better place in which to live.
Horst Weber.Grade Nine Graduation Banquet and Dance
This year’s graduation banquet started off punctually at 6:30 with the march of the graduands followed by 0 Canada, and grace by Mike Brown. A delicious cold plate meal was served. About half way through the first course we listened to a very enjoyable trumpet solo by Robert Hall. Heather Emery then proposed a toast to the school board followed by a reply from Mr. E.J. Kipp. The next item on the program was a vocai solo by Gloria Rogers and a toast was proposed by Gladys Brassard to the Parent's Association. The reply was by Mr. Walker, the president of the association. The next entertainer was Willard Roelofs with a clarinet solo. Ken Enander proposed a toast to the teaching staff to which Mr. Charnetski reolied. Donna Huber sang a solo followed by Mr. Thorlacius with a toast to the graduands. Horst Weber delivered a very interesting valedictory address after which the chairman, Pat Bartlett ore- se.nted Mr. Turner with a picture from the 1960-61 graduating class. Mr. Turner then gave a talk about the method by which 'Winston Churchill is run. The chairman then officially declared the banquet as closed. A dance followed at the L.C.I. beginning at 9:00 and ending at 12:00. The dance was attended by the graduands from Paterson, Hamilton and Churchill and the Playland Orchestra was in attendance. Flowers were presented to Mrs. Kioo, Mrs Kyle and Mrs. Bussara.
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This year has proven to be a year of disappointment for our senior boy's basketball team. Although we didn't win a championship spot, we have learned how to be good losers. Mainly because we don't know what it's like to be the winners.
Thanks to Mr. Doram, we were able to have a team this year, and put up a good fight at times. His own basketball exoerience has been, and wiii, be a great asset to us. Only through his determination will we be able to have a good ball team. Next year, he will make this school oroud of the senior boy's basketball team.
TEAM MEMBERS
L to R Rick Petrie, Trevor Norlin, John Wellman, Allan Wilkie, Ivor Carleton A. Doram
L to R Jerry Gangur, Bob Slobodian, Don Allen, Mike Onofrychuk, Nick Tkachenko, Bryan Reid
Senior Boy's Basketball
Junior Boy's Basketball
The Junior Boy's Basketball team has a successful season considering the fact that they are a first year team. Although greatly outplayed in some games, the team managed third place in the league standings, a . few ooints ahead of Paterson. The boys were at their best during the last half of the season.
However, they lost their semi-final games to St. Francis. Under the excellent coaching of Mr. McCormick, the team played very well.
TEAM MEMBERS
L to R Don Wyrostock, W. McCormick, John Kruchkywich L to R Mike Brown, Henry Bosch, Dave Rowley, Ron Ohama, Bob Oslansky
The reason that some people get lost in thought is that it is unfamiliar territory.
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Senior Girl's Basketball
The runners and uniforms of the Girl's Basketball team have been locked away and their traditional good luck charms have been put away until next season. The basketball trips and all the practices of the past few months, have become a fond memory. Winston Churchill High School's first year in comoetitive Senior "B" Girl's Basketball has come to a close.
The Girl's Team was credited with one victory throughout the season. We can truly say that they tried very hard, showed great determination and took defeat in their stride. The idea behind comoetitive snorts is to bring about better sportsmanship for the oarticioants and it takes more of a show of good sportsmanship to lose a game than to win one.
Winston Churchill has a first year basketball team that any school would be proud of. We realize our team has great ootential and next year with more practice and the additional experience gained from this year, we hope to be very successful. Hr. Hiatt, the team's coach, deserves a snecial thanks, as he Dut in a great deal of time and effort towards shaping the foundation for a championship team.
We'd like to thank the giris who played on this year's team and helped to make Churchill's debut into competitive sports a steeping stone to a brighter outlook for next year. We wish the following team the best of luck and hope that they can hit the basket more often than we did.
TEAM MEMBERS
L to R Gayle Brown, Katie Kozak, Sharron Grisak, C. Hiatt, Sharon Smeed, Sharlene Secretan, Carole Hughes.
L to R Maureen McAdam, Ivie Wallden, Frances Lowe, Donna Bogusky
Churchill junior Girl’s Basketball City Champions '60-'6l
Diana Crabb - (guard) her long shots won us many games.
Pat Coyle T (guard) leading point scorer in the play-offs.
Bev Jarvis - (forward) preferred to pass rather than shoot but was an
invaluable player.
Alice Herfst- (center) team captain and leading scorer.
Maureen Godsalve - (forward) a good guard and forward, "Mo" was an
outstanding player
Jean Perdue - (forward) the most improved player on the team. Jean was
a deadly rebounder
Edna Willis - (forward) her ability and willingness to play anywhere
made her invaluable
Delores Fraser - (guard) played well all season.
June Jacobson - (forward) was one of the best dribblers on the team. Elizabeth Harus- (forward) miesed the playoffs because of an injury
but supported the team 100%.
Thanks to a magnificent end-of-season run of success inspired by coach Sharon Smeed, the Junior Girls demolished Paterson in two games and then went on to beat Hamilton in two further games which were undecided until almost the last whistle.
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Harold Megland
Sr. Boy’s Badminton Chamoion
Diane Shimozawa 5 - Pin Bowling
Chamoion
Champion
Roger Mc/idam
Jr. Boy's Badminton
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SOCCER
The Church i'll Grade 9 Soccer Team shared the League Chamo ionshio with St Francis, but were beaten in the nlay-offs by Paterson Under the excellent coaching of Mr Flanagan, the team scored 10 goals while having only 3 scored against thejp. Out of the 8
Low detection of exon skipping in mouse genes orthologous to human genes on chromosome 22
No full textMagister Scientiae - MSc (Biochemistry)Alternative RNA splicing is one of the leading mechanisms contributing towards transcript and protein diversity. Several alternative splicing surveys have confirmed the frequent occurrence of exon skipping in human genes. However, the occurrence of exon skipping in mouse genes has not yet been extensively examined. Recent improvements in mouse genome sequencing have permitted the current study to explore the occurrence of exon skipping in mouse genes orthologous to human genes on chromosome 22. A low number (5/72 multi-exon genes) of mouse exon-skipped genes were captured through alignments of mouse ESTs to mouse genomic contigs. Exon-skipping events in two mouse exon-skipped genes (GNB1L, SMARCB1) appear to affect biological processes such as electron and protein transport. All mouse, skipped exons were observed to have ubiquitous tissue expression. Comparison of our mouse exon-skipping events to previously detected human exon-skipping events on chromosome 22 by Hide et al.2001, has revealed that mouse and human exon-skipping events were never observed together within an orthologous gene-pair. Although the transcript identity between mouse and human orthologous transcripts were high (greater than 80% sequence identity), the exon order in these gene-pairs may be different between mouse and human orthologous genes. Main factors contributing towards the low detection of mouse exon-skipping events include the lack of mouse transcripts matching to mouse genomic sequences and the under-prediction of mouse exons. These factors resulted in a large number (112/269) of mouse transcripts lacking matches to mouse genomic contigs and nearly half (12/25) of the mouse multi-exon genes, which have matching Ensembl transcript identifiers, have under-predicted exons. The low frequency of mouse exon skipping on chromosome 22 cannot be extrapolated to represent a genome-wide estimate due to the small number of observed mouse exon-skipping events. However, when compared to a higher estimate (52/347) of exon skipping in human genes for chromosome 22 produced under similar conditions by Hide et al.2001, it is possible that our mouse exon-skipping frequency may be lower than the human frequency. Our hypothesis contradicts with a previous study by Brett et al.2002, in which the authors claim that mouse and human alternative splicing is comparable. Our conclusion that the mouse exon-skipping frequency may be lower than the human estimate remains to be tested with a larger mouse multi-exon gene set. However, the mouse exon-skipping frequency may represent the highest estimate that can be obtained given that the current number (87) of mouse genes orthologous to chromosome 22 in Ensembl (v1 30th Jan. 2002) does not deviate significantly from our total number (72) of mouse multi-exon genes. The quality of the current mouse genomic data is higher than the one utilized in this study. The capture of mouse exon-skipping events may increase as the quality and quantity of mouse genomic and transcript sequences improves.South Afric
Low detection of exon skipping in mouse genes orthologous to human genes on chromosome 22
No full textMagister Scientiae - MSc (Biochemistry)Alternative RNA splicing is one of the leading mechanisms contributing towards transcript and protein diversity. Several alternative splicing surveys have confirmed the frequent occurrence of exon skipping in human genes. However, the occurrence of exon skipping in mouse genes has not yet been extensively examined. Recent improvements in mouse genome sequencing have permitted the current study to explore the occurrence of exon skipping in mouse genes orthologous to human genes on chromosome 22. A low number (5/72 multi-exon genes) of mouse exon-skipped genes were captured through alignments of mouse ESTs to mouse genomic contigs. Exon-skipping events in two mouse exon-skipped genes (GNB1L, SMARCB1) appear to affect biological processes such as electron and protein transport. All mouse, skipped exons were observed to have ubiquitous tissue expression. Comparison of our mouse exon-skipping events to previously detected human exon-skipping events on chromosome 22 by Hide et al.2001, has revealed that mouse and human exon-skipping events were never observed together within an orthologous gene-pair. Although the transcript identity between mouse and human orthologous transcripts were high (greater than 80% sequence identity), the exon order in these gene-pairs may be different between mouse and human orthologous genes. Main factors contributing towards the low detection of mouse exon-skipping events include the lack of mouse transcripts matching to mouse genomic sequences and the under-prediction of mouse exons. These factors resulted in a large number (112/269) of mouse transcripts lacking matches to mouse genomic contigs and nearly half (12/25) of the mouse multi-exon genes, which have matching Ensembl transcript identifiers, have under-predicted exons. The low frequency of mouse exon skipping on chromosome 22 cannot be extrapolated to represent a genome-wide estimate due to the small number of observed mouse exon-skipping events. However, when compared to a higher estimate (52/347) of exon skipping in human genes for chromosome 22 produced under similar conditions by Hide et al.2001, it is possible that our mouse exon-skipping frequency may be lower than the human frequency. Our hypothesis contradicts with a previous study by Brett et al.2002, in which the authors claim that mouse and human alternative splicing is comparable. Our conclusion that the mouse exon-skipping frequency may be lower than the human estimate remains to be tested with a larger mouse multi-exon gene set. However, the mouse exon-skipping frequency may represent the highest estimate that can be obtained given that the current number (87) of mouse genes orthologous to chromosome 22 in Ensembl (v1 30th Jan. 2002) does not deviate significantly from our total number (72) of mouse multi-exon genes. The quality of the current mouse genomic data is higher than the one utilized in this study. The capture of mouse exon-skipping events may increase as the quality and quantity of mouse genomic and transcript sequences improves.South Afric
New Algorithms for EST clustering
No full textPhilosophiae Doctor - PhDExpressed sequence tag database is a rich and fast growing source of data for gene expression analysis and drug discovery. Clustering of raw EST data is a necessary step for further analysis and one of the most challenging problems of modem computational biology. There are a few systems, designed for this purpose and a few more are currently under development. These systems are reviewed in the "Literature
and software review". Different strategies of supervised and unsupervised clustering are discussed, as well as sequence comparison techniques, such as based on alignment or oligonucleotide compositions. Analysis of potential bottlenecks and estimation of computation complexity of EST clustering is done in Chapter 2. This chapter also states the goals for the research and justifies the need for new algorithm that has to be fast, but still sensitive to relatively short (40 bp) regions of local similarity. A new sequence comparison algorithm is developed and described in Chapter 3. This algorithm has a linear computation complexity and sufficient sensitivity to detect short regions of local similarity between nucleotide sequences. The algorithm utilizes an asymmetric approach, when one of the compared sequences is presented in a form of oligonucleotide table, while the second sequence is in standard, linear form. A short window is moved along the linear sequence and all overlapping oligonucleotides of a constant length in the frame are compared for the oligonucleotide table. The result of comparison of two sequences is a single figure, which can be compared to a threshold. For each measure of sequence similarity a probability of false positive and false negative can be estimated. The algorithm was set up and implemented to recognize matching ESTs with overlapping regions of 40bp with 95% identity, which is better than resolution ability of contemporary EST clustering tools This algorithm was used as a sequence comparison engine for two EST clustering programs, described in Chapter 4. These programs implement two different strategies:
stringent and loose clustering. Both are tested on small, but realistic benchmark data sets and show the results, similar to one of the best existing clustering programs, 02_cluster, but with a significant advantage in speed and sensitivity to small overlapping regions of ESTs. On three different CPUs the new algorithm run at least two times faster, leaving less singletons and producing bigger clusters. With parallel
optimization this algorithm is capable of clustering millions of ESTs on relatively inexpensive computers. The loose clustering variant is a highly portable application, relying on third-party software for cluster assembly. It was built to the same specifications as 02_ cluster and can be immediately included into the STACKPack package for EST clustering. The stringent clustering program produces already
assembled clusters and can apprehend alternatively processed variants during the clustering process
Ancient Genes in Cancer Gene Expression?
No full text>Magister Scientiae - MScBacksround: The Cancer/testis (CT) antigens are a division of germ cell specific genes not expressed in somatic cells, exceptions being placental cells and 20Vo - 4OVo of cancer types. The aptitude of CT antigens to elicit humoral immune responses, their restricted expression profile, absence of major histocompatability complex expression in male germline cells have contributed to the emergent attraction of CT antigens as ideal, prospective cancer vaccination candidates. Motivation: Presently there are M CT gene families containing a total of 97 gene products and isoforms. Due to the promulgation in sensitivity and specificity of rapid serological immunodetection assays e.g. serial analysis of recombinant cDNA expression libraries (SEREX), the magnitude of novel CT genes and gene families will increase. Hence, characteization of this unique subset of CT genes is fundamental to our erudition of this rapidly emerging novel subset of genes.
Obiectives: The sequencing of the human genome provides a useful biological framework for the categoization and systematization of rapidly accumulating biological information. A genomic approach was used to ascertain the locations of the CT genes in the human genome and determine if the genomic locations of the CT genes is nonrandom. An in-silico expression study was conducted for the CT genes with the aim of establishing if CT gene expression is restricted to the testis. A portion of the human genome housing the largest proportion of the CT genes was selected for analysis in order to determine if the surrounding genomic architecture influences CT gene expression. A comparative genomics approach was used in determining if the CT genes are "ancient genes
Fiander, Winston. Interview about Play and Games during his childhood in Coomb's Cove, Fortune Bay
No full textRounders; Location of Coomb's Cove; Sliding; Hide and seek; Model sailboat racing; Rowing and sailing his punt; Rescue of a fisherman; Dories; Bicycles; Swimming; Playing outdoors; Snow houses; Pedlar Joe (piddly); Slingshots; Breaking the neighbour's window; Tokens; Ice hockey; Making hockey sticks. Phone interview
"Development and implementation of ontology-based systems for mammalian gene expression profiling"
No full textPhilosophiae Doctor - PhDThe use of ontologies in the mapping of gene expression events provides an effective and comparable method to determine the expression profile of an entire genome across a large collection of experiments derived from different expression sources. In this dissertation I describe the development of the developmental human and mouse e VOC ontologies and demonstrate the ontologies by identifying genes showing a bias for developmental brain expression in human and mouse, identifying transcription factor complexes, and exploring the mouse orthologs of human cancer/testis genes. Model organisms represents fundamental aspects of mammal biology phenomena between model organism
is complex and it is to be the meaningful, a simplified representation can be a powerful means for comparison illustrated here in two ways.
Firstly, the ontologies have been used to illustrate methods to determine clusters of genes showing tissue-restricted expression in humans. The identification of tissue-restricted genes within an organism serves as an indication of the finetuning in the regulation of gene expression in a given tissue. Secondly, due to the differences in human and mouse gene expression on a temporal and spatial level, the ontologies were used to identify mouse orthologs of human cancer/testis genes showing cancer/testis characteristics. With the use of model systems such as
mouse in the development of gene-targeted drugs in the treatment of disease, it is important to establish that the expression characteristics and profiles of a drug target in the model system is representative of the characteristics of the target in the system for which it is intended
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