An estimated 5-10% of breast cancers are hereditary in nature and are due to the presence of a mutation in a breast cancer predisposition gene; approximately half of these cases possess a mutation in BRCA1 or BRCA2. Many BRCA1/BRCA2 mutations result in a truncated protein and hence are unequivocally disease-causing. However another class of mutations, the Variants of Unknown Significance (VUS), are more problematic as the effect of these mutations on protein function is unclear. The inability to classify these mutations as disease causing generates significant problems in risk evaluation, counseling and preventive care. Accordingly we sought to determine whether carriers of either a BRCA1 or BRCA2 mutation could be identified from non-carriers based on the gene expression patterns of non-cancerous cells. EBV-transformed lymphoblastoid cell lines established from BRCA1/BRCA2 mutation carriers and normal individuals were obtained through the NIH Breast Cancer Family Registries. Cell lines were mock-irradiated or treated with ionizing radiation (2 Gy). Following a recovery period of 6 hours total RNA was extracted and whole genome gene expression profiling was carried out. Molecular classifiers comparing the baseline expression profiles and the radiation-dependent expression profiles of BRCA1/BRCA2 mutation carriers to control individuals were created using a Support Vector Machine (SVM) coupled with a recursive feature removal (RFR) algorithm. Our results suggest that cell populations derived from BRCA1/BRCA2 mutation carriers display unique expression phenotypes from those of control individuals in both the basal and radiation-induced cases. In the task of classification using baseline expression, the BRCA1-classifier correctly classified 15/18 test samples using feature selection based on the training set only, while feature selection using the entire dataset (AD) improved classification to 16/18 samples. The BRCA2-baseline classifier correctly classified 13/17 and 14/17 (AD) samples, respectively. In the task of radiation-dependent classification, the BRCA1-IR classifier correctly classified 12/18 and 16/18 (AD) test samples respectively while the BRCA2-IR classifier correctly classified 13/17 and 16/17 (AD) test samples respectively. These results suggest the possibility of development of this assay into a novel hereditary breast cancer screening diagnostic able to accurately identify the presence of BRCA1 or BRCA2 mutations via a functional assay thereby improving patient outcomes. / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2008-03-27 15:38:19.269 / Canadian Breast Cancer Foundation-Ontario Chapter, Department of Pathology & Molecular Medicine Clinical Trust Fund

We introduce a novel Syntax-based Security Testing (SST) framework that uses a protocol specification to effectively perform security testing on text-based communication protocols. A protocol specification of a particular text-based protocol under-tested (TPUT) represents its syntactic grammar and static semantic contracts on the grammar. Mutators written in TXL break the syntactic and semantic constraints of the protocol specification to generate test cases. Different protocol specification testing strategies can be joined together to yield a compositional testing approach. SST is independent of any particular text-based protocols. The power of SST stems from the way it obtains test cases from the protocol specifications. We also use the robust parsing technique with TXL to parse a TPUT. SST has successfully revealed security faults in different text-based protocol applications such as web applications and kOganizer. We also demonstrate SST can mimic the venerable PROTOS Test-Suite: co-http-reply developed by University of Oulu. / Thesis (Ph.D, Computing) -- Queen's University, 2010-04-30 16:01:18.048

Genetics is concerned with inheritance, genomics with the study of genomes. Bioinformatics provides the tools to study the interface between the two. If a particular locus in the human genome could have 100 discrete alleles, then the genome (comprising an estimated 80,000 genes), could harbor 8 million different alleles. To record information about each of these alleles in a meaningful and systematic fashion is a task for the Mutation Database domain of bioinformatics. The HUGO Mutation Database Initiative is an international effort to capture, record and distribute information about variation in genomes. This initiative comprises a growing number of Locus-Specific Mutation databases, and a few large Federated Genomic databases [Cotton et al., 1998]. / Here I present work on a well recognized prototypical Locus-Specific database: PAHdb. PAHdb is a relatively large curated relational database. / This graduate project has had two major aims: to improve PAHdb , by careful analysis of version 1.0 and revision of its design, resulting in PAHdb version 2.0; to document the redesign process and share the experience by the conception of guidelines for content and structure of mutation databases in general. (Abstract shortened by UMI.)

Les algèbres amassées sont très intéressantes, entre autre du point de vue de la théorie des représentations. Leurs côtés combinatoires sont immenses et on a probablement seulement effleuré le sujet. Dans ce mémoire, nous allons amorcer l'étude d'une propriété combinatoire pour un cas particulier d'algèbres amassées. Nous espérons que notre travail jettera les bases pour l'étude du cas général. Notre but sera de prouver le théorème suivant: Théorème 0.1. Tous les carquois acycliques et connexes à trois sommets ant un nombre fini de suites maximales vertes. Nous allons done expliquer tout ce qu'il y a à savoir sur les carquois et par la suite, présenter la preuve de ce théorème. Comme supplément, nous donnerons en plus la liste complète de toutes les suites maximales vertes possibles pour ces carquois.

Treatment success often depends on the availability of accurate and reliable diagnostic assays to guide clinical practitioners in their treatment choices. An optimal test must excel in specificity and sensitivity, and depending on the application area time, low-cost and simplicity are equally important. For instance, time is essential in infectious diagnostics but this is less important in non-invasive prenatal testing (NIPT). In NIPT, specificity and sensitivity are the most important parameters. In this thesis I describe the development of four different methods, all based on padlock probes and rolling circle amplification, intended for molecular diagnostics. Application areas range from infectious disease diagnostics to NIPT and oncology. The methods described have in common that they overcome certain limitations of currently available assays. This thesis includes two new assays targeting infectious agents: one assay specifically detecting a highly variable double stranded RNA virus and the second assay demonstrating a new format of antibiotic susceptibility testing, which is rapid and generally applicable to different pathogens. Furthermore, I describe the development of a method that uses methylation markers to enrich fetal DNA, accurately quantify chromosome ratios and thus, detecting trisomy 21 and 18. The fourth method described in this thesis uses gap-fill ligation of padlock probes to detect diagnostic relevant point mutations with high specificity in situ. The assays presented have the potential, after automation and successful validation and verification studies, to be implemented into clinical practice. Furthermore, these assays demonstrate the wide applicability of padlock probes which, due to their properties in regard to specificity and multiplexity, are useful tools for nucleic acid detection in vitro as well as in situ. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>

Apie 5–10 proc. visų krūties navikų atvejų sudaro paveldimas vėžys. BRCA1 ir BRCA2 genai yra patys svarbiausi polinkį susirgti krūties vėžiu sąlygojantys genai. Kiti reikšmingai su padidėjusia krūties navikų išsivystymo rizika susiję – CHEK2 ir NBS1 genai. Šiame darbe ištirtos paveldimos dažniausiai Europos regione nustatomos šių genų mutacijos. Nustatytas BRCA1 ir CHEK2 genų mutacijų dažnis tarp jaunų krūties vėžiu susirgusių moterų, ištyrinėtos jų sąsajos su pacientės amžiumi, naviko klinikinėmis ir morfologinėmis savybėmis. Išanalizuota šeiminės anamnezės prognozinė vertė nustatant paveldimus BRCA1 ir CHEK2 genų pokyčius. Pirmą kartą Lietuvoje įsisavintas CHEK2 bei NBS1 genų tyrimas, nustatyta, kokios CHEK2 geno mutacijos dažniausios. Nors NBS1 geno mutacijų nerasta, bet įsisavinta metodika, kuri bus panaudota ateities tyrimams. Sukurtas kompleksinis BRCA1 bei CHEK2 genų mutacijų radimo prognozavimo modelis. Šiandien klinikinėje praktikoje panašūs modeliai naudojami įvertinti BRCA1/2 genų mutacijų tikimybę. Jų pritaikomumas ir specifiškumas skirtingose etninėse grupėse gali skirtis. Naudojant tirtų pacienčių charakteristikas, įtraukiant ne tik šeiminę anamnezę, pacientės ypatybes, bet ir klinikinius bei molekulinius navikų požymius, sukurti mūsų regionui pritaikyti modeliai bei nustatyti kriterijai, kurie padės atrinkti pacientes genetiniam konsultavimui dėl BRCA1 bei CHEK2 genų mutacijų. Šis naujas požiūris turi didžiulę praktinę naudą. / Approximately 5–10% of all breast cancer cases are considered to be hereditary. BRCA1 and BRCA2 genes are the most important breast cancer predisposing genes. Other genes significantly linked with an increased risk of breast tumors are CHEK2 and NBS1 gene. In this scientific work were studied the most prevalent in European region mutations of these genes. The rate of BRCA1 and CHEK2 gene mutations in young women with breast cancer was evaluated and the relationships between these mutations and patient's age, clinical and morphological tumor features are examined. The prognostic value of family history was analyzed when forecasting hereditary BRCA1 and CHEK2 gene mutations. For the first time in Lithuania the CHEK2, NBS1 genes tests were applied and the evaluation of which CHEK2 gene mutations are most prevalent was obtained. Although NBS1 gene mutations were not found, but applied test technique will be used in future research. There was created a prognostic model for determination of BRCA1 and CHEK2 gene mutations. In today's clinical practice similar models are used to assess the likelihood of the BRCA1/2 mutation. Their applicability and specificity in different ethnic groups may vary. Applying the studied data there was created a model adapted to our region. Testing patients, there were considered not only family medical history and personal characteristics, but also the clinical and molecular features of tumors. The criteria have been found which will help in selecting... [to full text]

This project was designed to investigate the impact of natural levels of ultraviolet-B radiation on the genomic mutation rate in Arabidopsis thaliana. UV-B radiation is a known mutagen, but plants may have evolved mechanisms to cope with any genomic damage induced by routine exposure to this radiation. In an attempt to determine whether the genomic mutation rate in a plant species is elevated in the presence of UV-B, two eleven generation mutation accumulation studies were preformed. One study incorporated levels of UV-B similar to that encountered on a clear mid-summer's day, while the other was performed in the absence of this mutagen. Mutation rate estimates, obtained primarily from maximum likelihood analysis of phenotypic data, were not significantly greater than zero, both in the presence and absence of UV-B. No evidence was found to support the notion that the genomic mutation rate is increased by exposure to natural levels of UV-B.

Evaluating the evolutionary role of mutations depends on an understanding of their major properties, including their rate of origin, U, and the distribution of their fitness effects, f(s). While substantial effort has been put into measuring these properties, most studies have only examined their distributions in a single context. In nature, spontaneous mutations are likely to experience heterogeneity in genetic and environmental context, and this could lead to variation in both U and f(s). My thesis investigates the changes in U and f(s) with different genetic and environmental factors in Drosophila melanogaster, in order to elucidate the nature of context-associated variation in mutational properties. Examination of condition-dependent variation in DNA repair showed that high and low conditioned individuals differ in the use of alternative repair pathways. This could ultimately lead to variance in their heritable mutation rates. However, the assumption that condition dependence in repair arises solely due to a presumed trade-off between accuracy and the energetic costs associated with different repair pathways is too simplistic. Instead, physiological considerations appear to mediate condition-dependent changes in DNA repair. Measurements of selection on individual mutations across different genetic and environment contexts showed that context-associated changes in mutational fitness effects are common. I found that heterogeneity in fitness effects across different environments result in changes to the overall mean and variance of f(s). This does not, however, seem attributable to the degree of ‘adaptedness’ of a population to a particular environment (a prediction generated by previous theoretical analysis). On the other hand, f(s) appears to be relatively robust to differences among genotypes, with epistasis averaging close to zero. This finding suggests that genetic and environmental perturbations may affect mutations differently. Overall, my thesis represents the most rigorous empirical investigation to date of the conceptual and theoretical predictions regarding the nature of context-dependent heterogeneity in U and f(s) for multicellular eukaryotes.

The coverage of a test suite is often used as a proxy for its effectiveness. However, previous studies that investigated the influence of code coverage on test suite effectiveness have failed to reach a consensus about the nature and strength of the relationship between these test suite characteristics. Moreover, many of the studies were done with small or synthetic programs, making it unclear that their results generalize to larger programs. In addition, some of the studies did not account for the confounding influence of test suite size. We have extended these studies by evaluating the relationship between test suite size, block coverage, and effectiveness for large Java programs. Our test subjects were four Java programs from different application domains: Apache POI, HSQLDB, JFreeChart, and Joda Time. All four are actively developed open source programs; they range from 80,000 to 284,000 source lines of code. For each test subject, we generated between 5,000 and 7,000 test suites by randomly selecting test methods from the program's entire test suite. The suites ranged in size from 3 to 3,000 methods. We used the coverage tool Emma to measure the block coverage of each suite and the mutation testing tool Javalanche to evaluate the effectiveness of each suite. We found that there is a low correlation between block coverage and effectiveness when the number of tests in the suite is controlled for. This suggests that block coverage, while useful for identifying under-tested parts of a program, should not be used as a quality target because it is not a good indicator of test suite effectiveness.

The integrity of the genome is critical to organisms and it is affected by many factors. Radiation, for example, poses a serious threat to genome stability of human beings. While physical monitors for radiation hazard are present, the biological consequences of long term exposure to radiation are not well understood. With the opportunity as part of the International Caenorhabditis elegans Experiment-1 flight project, several approaches using C. elegans were taken to measure mutational changes that occurred during the spaceflight. Among these methods, the eT1 balancer system was demonstrated to be well-suited as an integrating biological dosimeter for spaceflight. The dog-1 gene in C. elegans is required to prevent mutations at poly-G/poly-C tracts, and previous work has described that in the absence of DOG-1, small deletions initiate within these tracts, most likely as a consequence of improperly repaired replication blocks. The eT1 balancer system was adapted to investigate the broad mutational spectrum of dog-1 mutants. Using this system, I was able to determine a forward mutation rate of approximately 1 x 10-3, 10 fold higher than spontaneous. Both small deletions as reported previously and unreported large chromosome rearrangements were observed, and most of mutations analyzed are associated with G/C tracts. Thus, I propose that following dog-1-induced replication blocks, repair leads to a wide range of mutational events and chromosomal instabilities, similar to those seen in human cancers. The existence of the G/C tracts in C. elegans creates a fortuitous but perplexing problem. They are hotspots for genome instability and need enzymatic protection. In the genome of C. elegans, approximately 400 G/C tracts exist and are distributed along every chromosome in a non-random pattern. G/C tracts are also over-represented in another Caenorhabditis species, C. briggsae. However, the positions and distribution differ from those in C. elegans. Furthermore, in C. elegans, analysis of SAGE data showed that the position of the G/C tracts correlated with the level of gene expression. Although being a threat to genome stability, the genomic distribution of G/C tracts in C. elegans and their effect on regional transcription levels suggest a role for G/C tracts in chromatin structure.