Post-zygotic genetic variation has previously been shown in healthy individuals and linked to various disorders. The definition of post-zygotic or somatic variation is the existence of genetically distinct populations of cells in a subject derived from a single zygote. Structural changes in the human genome are a major type of inter-individual genetic variation and copy number variation (CNV), involving changes in the copy number of genes, are one of the best studied category of structural genetic changes. In paper I we reported a pair of healthy female monozygotic (MZ) twins discordant for aneuploidy of chromosomes X and Y, contributing to the delineation of the frequency of somatic variation in MZ twins. It also illustrates the plasticity of the genome for tolerating large aberrations in healthy subjects. In paper II we showed age-related accumulation of copy number variation in the nuclear genomes in vivo for both megabase- and kilobase-range variants. Using age-stratified MZ twins and single-born subjects, we detected megabase-range aberrations in 3.4% of people ≥60 years old but not in individuals younger than 55 years. Moreover, the longitudinal analysis of subjects with aberrations suggests that the aberrant cell clones are not immortalized and disappear from circulation. We also showed that sorted blood cells display different genomic profiles.  The detected recurrent rearrangements are candidates for common age-related defects in blood cells. This work might help to describe the cause of an age-related decline in the number of cell clones in the blood, which is one of the hallmarks of immunosenescence. In paper III we described a variable number tandem repeat (VNTR) ~4 kb upstream of the IFNAR1 gene, which was somatically variable.  We detected 14 alleles displaying inter- and intra-individual variation. Further analyses indicated strong clustering of transcription factor binding sites within this region, suggesting an enhancer. This putative VNTR-based enhancer might influence the transcriptional regulation of neighboring cytokine receptor genes and the pathways they are involved in. These three studies stress the importance of research on post-zygotic variation in genetics. Furthermore, they emphasize that biobanks should consider sampling of multiple tissues to better address this issue in the genetic studies.

The integrity of an organism's genome depends on the fidelity of DNA replication and the efficiency of DNA repair. The DNA mismatch repair (MMR) system, which is highly conserved from prokaryotes to eukaryotes, plays an important role in maintaining genome stability by correcting base-base mismatches and insertion/deletion (ID) mispairs generated during DNA replication and other DNA transactions. Mismatch recognition is a critical step in MMR. Two mismatch recognition proteins, MutSα (MSH2-MSH6 heterodimer) and MutSβ (MSH2-MSH3 heterodimer), have been identified in eukaryotic cells. MutSα and MutSβ have partially overlapping functions, with MutSα recognizing primarily base-base mismatches and 1-2 nt ID mispairs and MutSβ recognizing 2-16-nt ID heteroduplexes. The goal of this dissertation research was to understand the mechanism underlying differential mismatch recognition by human MutSα and MutSβ and to characterize the unique functions of human MutSα and MutSβ in MMR. In this study, recombinant human MutSα and MutSβ were purified. Binding of the proteins to a T-G mispair and a 2-nt ID mispair was analyzed by gel-mobility assay; ATP/ADP binding was characterized using a UV cross-linking assay; ATPase activity was measured using an ATPase assay; MutSα amd MutSβ’s mismatch repair activity was evaluated using a reconstituted in vitro MMR assay. Our studies revealed that the preferential processing of base-base and ID heteroduplexes by MutSα and MutSβ respectively, is determined by the significant differences in the ATPase and ADP binding activities of MutSα and MutSβ, and the high ratio of MutSα:MutSβ in human cells. Our studies also demonstrated that MutSβ interacts similarly with a (CAG)n hairpin and a mismatch, and that excess MutSβ does not inhibit (CAG)n hairpin repair in vitro. These studies provide insight into the determinants of the differential DNA repair specificity of MutSα and MutSβ, the mechanism of mismatch repair initiation, and the mechanism of (CAG)n hairpin processing and repair, which plays a role in the etiology and progression of several human neurological diseases.

Several oomycete species of the genus Saprolegnia are recognized as devastating fish pathogens and are responsible for the loss of millions of fish annually for the aquaculture industry. Until recently, these pathogens were kept in check using malachite green; however, due to its toxicity, this chemical has now been banned from use. Saprolegnia parasitica is recognized as the major pathogen of aquaculture fish species. The industry is struggling to predict and control S. parasitica outbreaks in fish hatcheries and there is a need for new knowledge regarding the population genetic structure of this pathogen. Random amplified microsatellites were used to compare isolates of S. parasitica collected from a variety of hatchery locations during the period of November 2009 - August 2011, in order to determine the level of genetic variability and determine changes in genetic diversity over time. Allele frequencies of scored characters were graphically compared. Population genetic diversity was measured using Nei’s genetic distance, Shannon’s Information Index, number of polymorphic loci and phylogenetic trees. Due to the presence of Saprolegnia parasitica in the facilities tested, it appears to be ubiquitous in aquaculture facilities and treatment and prevention will be an ongoing concern in aquaculture management. Overall, genetic diversity of S. parasitica isolates was determined to be low with at least some sexual recombination occurring over time. There was a diversity of genotypes collected from the same hatchery on a single day, indicating there was not a single genotype present at a given time point. Genetic profiling, such as used here, could provide facility managers with a new approach to develop a series of best practices to control sporadic outbreaks of disease. Use of these genetic markers and close monitoring of S. parasitica genotypes will permit early detection and sanitation protocols. / Graduate / 2015-04-24 / 0476 / 0792 / 0369 / cren06@uvic.ca

No description available.

The expansion of gene-specific trinucleotide repeats is responsible for a growing list of human disorders, including myotonic dystrophy type 1 (DM1). Repeat instability for most of these disorders, including DM1, is characterized by complex patterns of inherited and ongoing tissue-specific instability and pathogenesis. While the mechanistic basis behind the unique locus-specific instability of trinucleotide repeats is currently unknown, DNA metabolic processes are likely to play a role. My thesis involves investigating the contribution of DNA replication to the trinucleotide instability of myotonic dystrophy type 1. Herein I have designed an in vivo primate model system, based on the SV40 replication system, to assess the contribution of DNA replication to DM1 repeat instability. This system allows the assessment, under controlled conditions, and manipulation of variables that may affect replication-associated repeat instability, under a primate cellular system. Using the SV40 model system, I not only confirmed previous observations that repeat length and replication direction affect repeat instability, but also for the first time determined that the location of the replication origin relative to the repeat tract plays an important role in repeat instability. This novel observation allowed for the development of a fork-shift model of repeat instability, in which cis-elements adjacent to the repeat tract affect replication, in turn altering the propensity for repeat instability. To further my study of DNA replication in DM1 repeat instability, I have mapped the origin of replication adjacent to the DM1 locus in human patient cells and the tissues of DM1 transgenic mice actively undergoing repeat instability. The position of the replication origins adjacent to the repeat tract at the DM1 locus places several known cis-elements, including CTCF binding sites, in a position to alter replication as predicted by the fork-shift model. My analysis of the CTCF sites showed them capable of altering replication and repeat instability at the DM1 locus. Taken together these results suggest that the placement of replication origins, repeat tracts and cis-elements, may mark trinucleotide repeat tracts, such as the DM1, for locus-, tissue- and development-specific replication-associated repeat instability.

Women and men’s experiences and needs in relation to induced abortion, and their views on the prevention of unintended pregnancies were explored through questionnaire studies at 10 and13 Swedish women’s clinics (Papers I–IV). Among 798 women in age range 14 – 49, 35% had experience of at least one previous abortion, and in the age range 20 – 49, 41%. The risk factors for repeat abortion were having children (Odds Ratio [OR] = 2.57), lack of emotional support (OR 2.09), unemployment or sick leave (OR 1.65), tobacco use (OR 1.56), and low educational level (OR 1.5). Among 590 men in age range 16 – 63, 32% had been involved in at least one previous abortion. The risk factors were, being a victim of violence or abuse (OR 2.62), unemployment or sick leave (OR 2.58), and having children (OR 2.0). Tobacco use was common, among both women (33%) and men (50%), and among those with repeat abortion 41% and 57%, respectively. Some considered societal efforts important for prevention, (Paper I–II). Overall care-satisfaction (Paper III) was high (74% of women and 52% of men). For women, factors associated with high care-satisfaction were being well treated by the staff (OR 11.78), sufficient pain relief (OR 3.87), adequate information about the gynaecological examination (OR 2.25), suitable contraceptive counselling (OR 2.23), and accessibility to the clinic by phone (OR 1.91). For men, the factors were being well treated by the staff (OR 5.32) and adequate information about the abortion procedure (2.64). Existential experiences and needs related to abortion were investigated among 499 women. Three components were identified (Paper IV): existential thoughts (61% of women), existential practices (48%), and humanisation of the foetus (67%). A higher presence of existential components correlated with difficulty in deciding to abort and poor psychological wellbeing after the abortion. Interviews with 24 women and 13 men on their experiences and needs related to home abortion and views on the prevention of unwanted pregnancies revealed two overarching themes (Paper V). Home abortion increased autonomy: both women and men demonstrated self-care ability. However, autonomy was related to dependence: the desire to be treated with empathy and respect on equal terms and receive adequate information adapted to individual needs. They were motivated to avoid a subsequent abortion, but planned contraceptive follow-ups were rare. Both individual and societal challenges were implied: women and men experiencing repeat abortion appeared more disadvantaged and abortion involved complex aspects beyond medical procedures and routines. Thus, abortion care should be continuously evaluated to ensure care satisfaction, safety, and contraceptive adherence. Preventive efforts would include work opportunities, sex and relationship education, and cheap and effective contraceptives. Minimising differences between socioeconomic groups is important, and both individuals and society should share the responsibility for these efforts. / De senaste åren har kvinnor fått ökade möjligheter att välja mellan olika abortprocedurer, vilket medfört att andelen medicinska aborten har ökat och utgör 89% av alla inducerade aborter före utgången av graviditetsvecka 9. Den medicinska aborten kan avslutas i hemmet om kvinnan så önskar och inga hinder finns. Generellt finns begränsad kunskap om kvinnor och framför allt män som är involverade i en abort. Socialstyrelsens register ger endast information om; vilken vecka aborten avslutas i, abortmetod (medicinsk/ kirurgisk), kvinnans ålder, kommuntillhörighet, antal barn och tidigare aborter. Det innebär att det finns begränsad möjlighet att undersöka eventuella skillnader mellan olika grupper. En relativt hög andel (40%) av de abortsökande kvinnorna har erfarenhet av att ha gjort minst en tidigare abort, men kunskap om den gruppen är begränsad. Det övergripande syftet med den här avhandlingen var att undersöka kvinnors och mäns upplevelser och behov i samband med en abort och deras syn på förebyggande insatser. Kvantitativa och kvalitativa metoder har använts i de olika delarbetena (I– V) samt teoretiska modeller som utgår från folkhälso- och omvårdnadsperspektiv. Samtliga studier är godkända av den regionala etikprövningsnämnden i Uppsala. Delarbete I–IV bygger på resultat från en multicenter studie som genomfördes 2009, där 10 och 13 svenska kvinnokliniker deltagit. Syftet med delstudie I och II var att undersöka riskfaktorer för upprepad abort bland kvinnor och män. Två enkäter (kvinna/man) delades ut på kliniken i samband med att kvinnorna sökte för abort. Enkäten besvarades av 798 kvinnor efter genomgången abort. Männen som var involverade i graviditeten blev tillfrågade att delta i studien av kvinnorna och 590 män besvarade enkäten. Separata frankerade kuvert bifogades, vilket möjliggjorde att kvinnorna och männen kunde besvara enkäten oberoende av varandra. Resultatet i delarbete I och II visade att 35% av 798 kvinnor i åldern 14 – 49 hade erfarenhet av minst en tidigare abort och den andelen var högre i åldern 20 – 49; 41%. Upprepad abort var associerat med; att ha barn (Odds Ratio [OR] = 2.57), brist på emotionellt stöd (OR 2.09), att vara arbetslös eller sjukskriven (OR 1.65), rökning/snusning (OR 1.56), och låg utbildningsnivå (OR 1.5). För de 590 männen i åldern 16 – 63 hade 32% erfarenhet av minst en tidigare abort. Upprepad abort var associerat med; att ha varit utsatt för våld eller tvång (OR 2.62), att vara arbetslös eller sjukskriven (OR 2.58), och att ha barn (OR 2.0). Daglig tobaksanvändning var vanligt förekommande bland både kvinnor (33%) och män (50%), men vanligare bland dem med erfarenhet av upprepad abort (41%/57%). Konkreta åtgärder som kvinnor och män med aborterfarenhet efterfrågar i det förbyggande arbetet är fler arbetstillfällen, mer och bättre kvalitet på sexoch samlevnadsundervisningen i skolan, hög tillgänglighet till billiga och effektiva preventivmedel samt kvalificerad rådgivning. Slutsatserna i delarbete I och II är att kvinnor och män med erfarenhet av en abort löper hög risk för en upprepad abort. Personer med erfarenhet av upprepad abort är mer socioekonomiskt utsatta. Att minska skillnader mellan olika socioekonomiska grupper kan därför vara av betydelse i det förebyggande arbetet med oönskade graviditeter. Delarbete III syftade till att undersöka hur nöjda kvinnor och män upplevt vården i samband med en inducerad abort samt att identifiera faktorer som har samband med en hög grad av tillfredsställelse med vården. De flesta var nöjda med vården, men en fjärdedel (26%) av kvinnorna och nästan hälften av männen (48%) var inte helt nöjda. Den viktigaste faktorn för hög tillfredsställelse med vården var att ha fått ett gott bemötande bland både kvinnor (OR 11.78) och män (OR 5.32). Andra faktorer av betydelse var för kvinnorna att ha fått tillfredsställande; smärtlindring (OR 3.87), information om den gynekologiska undersökningen (OR 2.25), och preventivmedelsrådgivning (OR 2.23), samt att det var lätt nå kliniken via telefon (OR 1.91). För männen var även information om abortproceduren en viktig faktor för deras totala tillfredsställelse med vården (2.64). Slutsatserna i delarbete III är att en fjärdedel av kvinnorna och varannan man inte var helt nöjda, vilket indikerar att abortvården kan förbättras, speciellt avseende männen. Bland både kvinnor och män, är ett positivt bemötande från personalen den viktigaste faktorn för en tillfredsställande upplevelse av vården i samband med abort. Delarbete IV syftade till att undersöka förekomsten av existentiella tankar, känslor och handlingar bland 499 kvinnor som gjort en abort. Genom faktoranalys identifierades olika existentiella komponenter relaterade till en inducerad abort. Resultatet visade att sex av tio kvinnor hade existentiella tankar om livet, döden, mening och moral. Nästan hälften av kvinnorna uppgav att de hade behov att genomföra en symbolisk handling i relation till aborten, och 67% tänkte på fostret i termer av ett barn. Högre grad av existentiella faktorer korrelerade med större svårighet att fatta beslut om abort, och ett sämre psykiskt välbefinnande efter aborten. Slutsatserna i delarbete IV är att existentiella känslor, tankar och handlingar i samband med abort är vanligt förekommande. Detta är för vårdpersonalen en utmanande aspekt som inte självklart inkluderas i abortvården och dess styrdokument. Syftet med delarbete V, som var en kvalitativ studie, var att undersöka kvinnors och mäns upplevelser och behov i samband med hemabort. Syftet var även att belysa deras syn på samhälleliga åtgärder för att förebygga oönskade graviditeter. Kvinnorna rekryterades från fem olika kvinnokliniker och männen tillfrågades om att delta i studien genom kvinnorna. Tjugofyra kvinnor och 13 män intervjuades via telefon. Innehållsanalysen mynnande ut i två övergripande teman; autonomi som beskriver att beslutet om abort och valet av metod var väl genomtänkt av kvinnan, men oftast med stöd av partner. Hemmiljön ökade deras integritet och kontroll, vilket också underlättade deras möjligheter att fritt uttrycka och dela känslor; beroende som beskriver kvinnors och mäns önskan att bli behandlade med värdighet och respekt och att få tillfredsställande information som är individuellt anpassad för deras behov. Resultatet indikerar att hemabort ställer höga krav på vårdpersonalens kommunikationsförmåga. Kvinnor och män var motiverade att förebygga en ny oönskad graviditet men ett planerat återbesök var ovanligt. I det förebyggande arbetet av oönskade graviditeter ansågs fast arbete, förbättrad kommunikation/utbildning och subventionerade preventivmedel som viktigt. Slutsatserna i delarbete V är att hemabort ökar kvinnors och mäns autonomi, men samtidigt finns ett uttalat beroende av att vårdpersonalen utformar vården individuellt och med respekt för olika livssituationer. Rutiner och uppföljning bör därför kontinuerligt utvärderas för att säkerställa både kvaliteten av abortvården men också följsamheten i användningen av preventivmedel. Oönskade graviditeter och aborter är inte frågor som enbart berör kvinnor eller hälso- och sjukvården, det är större än så, ett delat ansvar som berör både individer och samhället.

Concern remains regarding the efficacy of drink driving countermeasures to produce lasting change for repeat offenders, as a wide array of countermeasures have been developed that demonstrate varying levels of success in reducing re-offence rates. This thesis proposes that the collection and examination of repeat offenders' self-reported perceptions, experiences and behavioural changes that result from completing court-ordered interventions can provide valuable contributions to the development of effective sentencing strategies. As a result, the program of research implemented a mixed-method design to investigate the self-reported impact of legal sanctions, a drink driving rehabilitation program, and alcohol ignition interlocks on key outcome measures for a group of recidivist drink drivers.----- Study One incorporated a cross-sectional design to examine the deterrent effect of traditional legal sanctions (e.g., fines and licence disqualification periods), non-legal sanctions, alcohol consumption, recent offending behaviour(s), and the actual severity of sanctions on perceptual deterrence and intentions to re-offend. The study involved face-to-face and telephone interviews with 166 repeat offenders. The analysis indicated that participants perceived legal sanctions to be severe, but not entirely certain nor swift.----- In Study One, self-reported recent drink driving behaviours and alcohol consumption levels were identified as predictors of future intentions to drink and drive. The results suggest that habitual behaviours are difficult to change, and heavy alcohol consumption levels increase the probability of re-offending. At a bivariate level, three non-legal sanctions were negatively associated with intentions to re-offend but were not predictors of future intentions to drink and drive in the model. In addition, a relationship was not evident between: (a) the size of the penalties and perceptions of sanction severity or future intentions to drink and drive, and (b) the number of previous convictions and self-reported deterrence. The findings of the study confirm the popular assumption that some repeat offenders are impervious to the threat and application of legal sanctions.----- Study Two examined the stages of change and self-efficacy levels of 132 repeat offenders - who were all involved in Study One - while they completed an 11 week drink driving rehabilitation program. A repeated measures design was implemented to focus on the impact of the intervention on a number of salient program outcomes such as participants' motivations and self-efficacy levels to control and change their drinking and drink driving behaviour(s). Prior to program commencement, the majority of participants were motivated to change their drinking driving, but not their drinking. The sample also reported high self-efficacy levels to control the two behaviours, but did not have high expectations of the effectiveness of the program.----- Upon completion of the program, significant increases were evident in motivations to change drinking and drink driving behaviours, and a large percentage of participants reported a positive appraisal of the effectiveness of the intervention. Program completion also resulted in a reduction in self-reported alcohol consumption levels, yet the majority of the sample continued to consume harmful levels of alcohol. Self-efficacy levels remained high, although a notable finding was that participants reported higher levels of control over their drinking rather than drink driving behaviours. In general, Study Two provided a positive perspective of the capacity of a drink driving rehabilitation program to produce change for a group of repeat offenders.----- Study Two extended a small body of research and examined the effects that mandated program enrolment has on motivations to change, as well as expectations and appraisals of program effectiveness. Contrary to predictions, mandated participants did not report lower levels of motivation to change drinking and drink driving compared to voluntary attendees, but did indicate lower expectations of the effectiveness of the program, as well as being willing to engage in the program. Furthermore upon program completion, mandated participants also reported lower appraisals of the effectiveness of the program, but this factor was not associated with intentions to re-offend or non-program completion. Rather, not successfully completing the program appeared linked with being unwilling to change drinking behaviours.----- Study Three involved a longitudinal case-study design that utilised both quantitative and qualitative data to conduct one of the first examinations of the impact of alcohol ignition interlocks on a group of recidivist drink drivers from a users' perspective. The study investigated 12 participants' self-reported perceptions and experiences of using an interlock and the effect that the device had on key program outcomes such as drinking levels, operational performance, circumvention attempts and general beliefs regarding the effectiveness of the device in comparison to traditional legal sanctions.----- Participants reported positive appraisals regarding the effectiveness of the device as qualitative themes emerged concerning the educational and practical benefits of interlocks. However, closer examination of individual interlock performances revealed each participant had attempted to start their vehicle after consuming alcohol, and a smaller sample of three drivers were regularly attempting to start their vehicle after drinking. The combination and analysis of self-reported and downloaded interlock data revealed four main themes: (a) initial operational difficulties, (b) a general unwillingness to reduce alcohol consumption levels, (c) an unwillingness to acknowledge/recognise that interlock breath violations resulted from drinking, and (d) an overall decline in the frequency of interlock breath violations over the interlock installation period. Similar to Study Two, a notable finding was that half the sample was still consuming harmful levels of alcohol upon program completion.----- Taken together, the results of the program of research highlight that repeat offenders' entrenched behaviours, such as drinking and drink driving, are resistant to change and that multi-modal interventions are required if the drinking and driving sequence is to be broken for this population. The findings have direct implications for the sentencing and management of repeat offenders and the development of countermeasures that attempt to produce long-term behavioural change.

Relaxin and insulin-like peptide-3 (INSL3) are closely related reproductive hormones that are derived from a common ancestor. Relaxin was initially named for its ability to relax the pubic symphysis in pregnant guinea pigs at parturition. Since then relaxin has been found to be involved in many physiological processes based on its ability to stimulate the breakdown and remodeling of collagen fibers. INSL3 is also known as Leydig insulin-like hormone and the relaxin-like factor, and is produced by the Leydig cells in the testis, the thecal and luteal cells of the ovary, the thyroid, placenta and mammary gland. INSL3 induces transabdominal testicular descent by stimulating the development of the gubernacular ligament, which subsequently swells and contracts to pull the fetal testes towards the inguinal wall. In adults however, evidence suggests that INSL3 is involved in reproductive function, acting to promote the survival of male and female germ cells.

[Truncated abstract] This thesis examines the phenomenon of repeat burglary and its significance for crime prevention, criminology and victimology. The research program for this thesis was inspired some time ago by the Kirkholt burglary prevention project in the United Kingdom. The reduction of repeat victimisation quickly came to be seen as the key to Kirkholt?s success and by the late twentieth century victim-based crime prevention projects had been implemented in many parts of the world. However, even though these projects have achieved notable success there is still intense debate about why one-time victims are more likely than others to become future victims. This thesis aims to increase understanding of repeat burglary and other forms of repeat victimisation by contributing to its key concepts and its methods of analysis, and by applying these insights in Australian settings. In pursuing this endeavour the thesis links the problems of repeat victimisation with problems in other areas of criminology and social science. In particular the issue of whether prior victimisation is a cause of future victimisation or merely a marker of pre-existing risk has analogs in the areas of offending, of employment, in international disputes, and in many others. Despite this, there has been limited transfer of methods and concepts between repeat victim researchers and researchers in other areas. The thesis examines repeat burglary as a substantive area of research, but its approaches to method, concepts and data are relevant to all repeat victimisation research. ... It draws together criminological theory, conceptual analysis, and a pioneering application of survival analysis to pursue the mechanisms underlying repeat burglary in a Perth suburb. In doing so it illuminates issues about the relative power of state dependence and heterogeneity explanations of repeat burglary and arrives at substantive results that in some aspects differ from findings in the United Kingdom. This section also argues that the concept of state dependence commonly adopted is iv unnecessarily constraining and that a broader concept can explain some potentially conflicting findings of repeat victimisation research. Section 3 is an evaluation of a victim-focused burglary prevention initiative in Adelaide one of two nationally supported pilot projects. Section 4 examines carefully the claimed advantages of victim-focused crime prevention for distributing burglary prevention resources in an efficient and equitable way. It examines evidence concerning the differential capacity and willingness of victims to take effective preventive action and the need for both individual and collective support for effective preventive initiatives. Section 5 concludes the thesis by arguing first that the merging of victim support and crime prevention is not as simple as is sometimes claimed. It also argues that crime prevention needs to take into account more than criminological theory if it is to be effective. An important argument of the conclusion is that criminological imagination has been overly limited in comprehending repeat victimisation, and it explores the ways in which criminological research still struggles to appreciate the importance of the victim for theory and crime prevention. It also argues that the implications of repeat victimisation have yet to be fully developed and accepted. Fuller details of the thesis structure are given at the end of the introduction.

Thesis (M.Sc.). / Written for the Dept. of Biochemistry. Title from title page of PDF (viewed 2008/12/10). Includes bibliographical references.