M.A. / Patterns of substance abuse within the family is a widespread phenomenon that occurs through generations. Although various factors can be a symptom of a dysfunctional family, the dynamics that maintain the transgenerational patterns of substance abuse are of great interest. The family in which the abuse of alcohol is repetitive through generations, is seen as a dysfunctional family system. It appears that a circular pattern exists in the family that maintains the alcohol abuse. Although the family as a whole has an influence on individual members, these individual members enter their families with their own preconceived mind maps of past experiences that also have a great influence on the family dynamics. Family dynamics are seen as those factors that impact either positively or negatively on the family and its individual members. The alcoholic parent and adult child of the alcoholic parent are the subjects of concern in this study because it is assumed that parental inputs have been the most influential in the respondent’s lives. A qualitative method of research was implemented to describe this explorative study and was decided on because it describes the phenomenon of transgenerational patterns of alcohol abuse from the viewpoint of the respondent. The aim of this research study was to determine the dynamics that contribute to transgenerational patterns of alcohol abuse, with specific reference to the respondent’s family history of alcohol abuse, their co-dependency (alcohol abuse) and the maintenance of these dynamics throughout generations. These dynamics will be explained in terms of the Living Systems Theory and the Object Relations Theory. These theories form the theoretical foundation from which these dynamics were explained. From these theories a strategy of data-gathering was developed with specific focus on the genogram, family tree and general questions. A focused sampling method was implemented in this research study, and the research units consisted of five respondents with families that have a history of alcohol abuse. Data-gathering was done through phenomenological and semi-structured interviews. The interviews were audiotaped and fieldnotes were made, although limited and only to confirm some of the findings of the research study. The data was analysed according to a specific strategy. Preliminary coding was done by using the audiotapes (transcriptions) and fieldnotes. After the preliminary coding was completed, these categories were used to derive central themes from the findings and all the categories were then divided under one or several of these themes. These central themes were compared with existing literature in order to confirm the findings of this research study and to enhance the trustworthiness. From the study, certain recommendations with regard to methodology and content were made. / Dr. E. Oliphant

"This thesis is a report on the feasibility of isolating a certain group of mutants. I call these mutants the "p.i.-related" mutants; an explanation of what they are and of my rule for grouping them together is given here. Bacterial chromosome replication consists of at least three steps: initiation, polymerization and termination/segregation (which may or may not comprise a single step). Inhibition of the polymerization step ("polymerization inhibition" or "p.i.") in a rapidly-growing bacterial population causes morphological distortion of the cells, a high death rate among them, and a number of other consequences. Recently, two great regulatory systems for bacterial cell behavior (described in Chapters IX and X) have been elucidated, and it appears that many of the consequences of p.i. might be explainable as the malfunctioning of these two systems. I define a "p.i.-related mutation" as a mutation that satisfies two criteria: First, it either causes p.i., mimics p.i., prevents p.i. or blocks the effects of p.i. Second, it exerts its effects by disrupting one of the two above-mentioned regulatory systems. The main question asked and answered in this report is: How good is each of three different methods of selection for p.i.-related mutants?"-- / Typescript. / "August, 1979." / "Submitted to the Department of Biological Science in partial fulfillment of the requirements for the degree of Master of Science." / Advisor: Johan H. Stuy, Professor Directing Thesis. / Includes bibliographical references (leaves 383-434).

Alopecia Areata (AA) is a highly prevalent autoimmune disease in the US with a lifetime risk of 2.1%. In AA, autoimmunity develops against the hair follicles, which leads to infiltration of immune cells around affected follicles. Among genetic risk factors in complex autoimmune diseases, variants cluster in genes regulating the immune response, as well as the target organ. AA is believed to result from both genetic and environmental factors. To identify underlying genetic drivers in AA, we analyzed AA risk genes using various sequencing techniques and analysis methods to identify causal variants and placed them in functionally relevant contexts using innovative mapping techniques. To address the role of variants in immune function, we studied the Interleukin-2 Receptor Alpha (IL2RA), which we identified as a significant locus to study genetic factors underlying immune function from our AA GWAS studies (p=1.74*10-12)11. IL2RA plays a crucial role in regulating immune tolerance and controlling activity of regulatory T cells (Treg)13. We identified significant causal variants in the IL2RA region associated with AA using GWAS, targeted resequencing, and custom capture exome sequencing approaches. We validated the expression of these variants in immune cell cluster tissue types in silico, and specifically in CD4+ T cells. The variant rs3118740 increases AA susceptibility for carriers of the C allele. Such allele specific effects could lead to a perturbation of Treg function, for example, one study in T1D where patients with the rs3118470 risk variant have Treg with IL-2 signaling defects14. These studies demonstrated that identifying causal variants may lead to an improved understating of Treg function and risk of autoimmunity in AA. Next, to study genetic susceptibility in the target organ in AA, the hair follicle (HF), the second candidate GWAS susceptibility gene we studied was peroxiredoxin 5 (PRDX5) (p= of 8.7*10-14), which is also a GWAS gene in Crohn’s disease, sarcoidosis, and psoriasis15,16. PRDX5 is a member of the family of antioxidant enzymes that are crucial for regulating oxidative stress. Our lab performed whole exome sequencing in 849 AA patients, together with selected custom capture regions of genomic sequencing. Using a test of variant enrichment, we identified variants in PRDX5 that were significant in both our GWAS and exome studies, and thus represented likely candidate causal variants. Using Bayesian fine mapping, we identified a GWAS and exome sequencing variant, rs574087, that was significantly enriched in both, and is predicted to be a causal variant in keratinocytes and melanocytes. To functionally validate PRDX5, we immunostained healthy human HF and AA affected HF, and found that PRDX5 is upregulated AA human HF. PRDX5 is expressed in cultured melanocytes by immunostaining, which is consistent with melanocytes exhibiting high levels of oxidative stress. We postulated that PRDX5 may be involved in protection from oxidative stress, and that its dysregulation may contribute to autoimmunity. Finally, along with genetic predisposition, environmental triggers such as the microbiome have emerged as potential factors contributing to pathologic immune responses in autoimmune diseases. To determine the role of the microbiome in AA pathobiology, we performed 16S rRNA sequencing of skin swabs, hair follicles, and stool samples from a cohort of 34 AA patients and 12 healthy controls (HCs). Unexpectedly, we found evidence of striking gut dysbiosis, consisting of over-representation of Firmicutes and under-representation of Bacteroides in the gut microbiome of AA patients compared with healthy subjects, but no significant differences in skin or hair follicle (HF) microbiome composition. To investigate the role of the gut microbiome in AA development in vivo, we depleted the gut microbiome in C3H/HeJ mice and found that the mice were largely protected from AA developing. These data revealed a requirement for gut microbiota in the onset of murine AA. Taken together with recent reports in the literature of reversal of AA in several patients following fecal microbiota transplant (FMT)17,18, our findings suggest that restoring homeostasis of the gut microbiome may represent an effective new treatment modality in the management of AA.

Triticale (x Triticosecale Whitm.) is a cereal with favorable agronomic traits for a Canadian bioproduction platform crop. Appropriate tissue sampling times were determined and gene expression profiles were evaluated in five triticale seed tissues and eleven vegetative tissues using the Affymetrix Wheat GeneChip®. Genes that were expressed, not expressed, tissue-specific, tissue-enriched and developmentally regulated were identified. The percentage of probe sets on the wheat GeneChip with gene ontology annotations was improved from less than 3% to over 76% using homologous sequence identification and annotation transfer. This information was used to determine functions and processes over-represented within the identified gene lists and provide biological meaning to the results. Expression of candidate genes was further evaluated using qRT-PCR, RNA in situ hybridization and promoter characterization. This study has provided a comprehensive triticale gene expression atlas; knowledge regarding triticale development, gene function, expression and regulation; and tools enabling further triticale research and development. / xxiii, 425 leaves : col. ill. ; 29 cm

Change in Modified Contemporary Comparison proofs during first and second crop period was computed from up to eight proofs during both periods for AI and non-AI sampled Holstein bulls with repeatability of last evaluation≥.90. Effect of proof number within testing period on the bull's milk or fat evaluation was estimated with bull absorbed. AI and non-AI sampled bulls' proofs increased from initial first crop proof and then remained fairly constant during the remainder of first crop period. With inclusion of second crop daughters, proofs dropped significantly more for non-AI than AI sampled bulls. This drop increased for non-AI sampled bulls born after 1976, but was unchanged for AI sampled bulls. A measure of change was calculated using last second crop proof minus the second to last first crop proof. Expected standard deviation of change was calculated and used to stratify bulls into eight change classes. A larger proportion of non-AI sampled bulls have proofs that dropped than could be explained by chance alo e. Results indicated that non-AI sampled bulls were less stable than AI sampled bulls' proofs and that stability of non-AI sampled bulls has diminished over time. For one of the studs that had stability of their bulls' proofs examined, their young sire sampling program was investigated. Individual phenotypic and genetic records of first crop and non-first crop cows in 3449 herds participating in the AI stud's young sire sampling program from 1971 to 1987 were used to characterize the sampling program, to estimate genetic trend across and within the progeny test herds, and to compute within herd means and standard deviations of various traits (herd characteristics). Herd characteristics of progeny test herds were utilized in predicting within herd genetic trend d in predicting changes in proofs of bulls sampled by the stud. For bulls sampled by this stud, average herd characteristics and variability of herd characteristics across the contributing herds was calculated and used to predict the measure of proof change in the first study. Average herd-year characteristics and variability of herd-year characteristics explained 39% to 46% of the variation in milk. and fat proof changes. In general, variability of herd-year characteristics and average within herd-year standard deviation herd-year characteristic variables explained most of the changes in proofs. Genetic trend across the progeny test herds was large for milk (105 kg) and fat (3.1 kg) yield. Genetic trend computed from PTAs of sires of first crop cows increased 58 kg milk and 1.5 kg fat per year from 1971 to 1978 and 176 kg milk. and 5.5 kg fat per year from 1979-87. The genetic level of daughters of young sires born after 1983 was equivalent or exceeded the genetic level of cows from other sires in the herd. Results indicated that within herd genetic improvement will not be hurt and may actually be enhanced from participating in a young sire sampling program depending upon sire selection of cows not bred to young sires. Herd characteristics explained forty-five and fifty-one percent of the differences in within herd genetic trends for milk and fat yield, respectively. Average sire PTA of non-first crop daughters accounted for 80% and 67% of the explainable differences. Other herd characteristics indicated that herds with larger within herd standard deviation milk yields, larger number of young sires represented, younger cows, less average days open, and greater percentage of cows sired by AI sires made faster rates of genetic improvement. / Ph. D.

A systematic study of a collection of Lon⁻ mutants has been made in order to determine whether their pleiotropic phenotype is due to mutations affecting one or more genes. A fine structure map of the lon locus was constructed by Pl mediated generalized transduction. The lon⁻ mutations were found to map in two "clusters" within the region. Phenotypic characterization of a set of isogenic Lon⁻ strains derived from these experiments indicated that all Lon-associated phenotypes (e.g. sensitivity to UV irradiation, decreased ability to inherit plasmid and prophage, abnormal polypeptide degradation and regulation of capsular polysaccharide biosynthesis) are differentially expressed in Lon⁻ strains. A direct correlation exists between the intracistronic ordering of the lon⁻ alleles and the degree of expression the Lon⁻ phenotypes in each strain. All isogenic Lon⁻ strains exhibit conditional lethality upon a nutritional shift-up. However, some filamenting Lon⁻ mutants are not able to overcome this defect when exposed to growth conditions known to promote cell division in Lon⁻ strains. Evidence was obtained that suggest a role for nucleotide pools in the control of cell division and capsular polysaccharide production. Reversion studies indicated that all lon⁻ mutations studied are point mutations. The failure to generate deletions of the lon region in χ573, an F' strain carrying the lac to minE region on the plasmid, and the inability to cure F' strains carrying a lon⁻ mutation on the plasmid suggest that the lon gene product may be indispensable for the cell's survival. From transductional crosses, two intermediate phenotypic classes: UV-resistant, mucoid (UV^RMuc), (Class A) and UV-sensitive, nonmucoid (UV^SRou) (Class B), were obtained that did not segregate colonies of the opposite morphology. Genetic analysis of these strains by back-transduction into a proC⁻ lon⁺ background, indicated that complete genetic separation of all Lon-associated phenotypes tested was not achieved, although differences in the expression of some of these persisted. Data obtained from complementation analysis ruled out the presence of two genes at the lon locus. The patterns of complementation observed were compatible with the existence of one lon gene, having at least two distinct domains, and whose product is a multifunctional polypeptide. / Ph. D.

Submitted by admin tede (tede@pucgoias.edu.br) on 2017-06-29T13:18:42Z No. of bitstreams: 1 MARIA JOSÉ BATISTA DE SOUSA.pdf: 2843064 bytes, checksum: f400a0df10a20e086f4f74a5b6cf9480 (MD5) / Made available in DSpace on 2017-06-29T13:18:42Z (GMT). No. of bitstreams: 1 MARIA JOSÉ BATISTA DE SOUSA.pdf: 2843064 bytes, checksum: f400a0df10a20e086f4f74a5b6cf9480 (MD5) Previous issue date: 2017-03-28 / The species Brosimum gaudichaudii (family Moraceae) and Caesalpinia ferrea (family Fabaceae) are widely distributed throughout Brazil and are considered medicinal plants. The extract of Brosimum gaudichaudii bark has been indicated for the treatment of skin blemishes and vitiligo. On the other hand, the extract of Caesalpinia ferrea fruit has been used due to its therapeutic properties as antibacterial, anti-inflammatory and analgesic action. Much of the medicinal plant extracts constituents are unknown and may be toxic to human and animal health, so it is necessary to study the qualitative phytochemical of secondary metabolites and to evaluate the cytotoxic, genotoxic and mutagenic potential of the extracts of these species. In this study, in order to evaluate the mutagenic and / or genotoxic effects, different concentrations of the extractive solutions of B. gaudichaudii and C. ferrea were evaluated in vivo in Astyanax sp and Allium cepa, and ex vivo, by the micronucleus test in T lymphocytes humans. Data were submitted to Kruskall-Wallis a non-parametric test and then to simple linear regression with a significance level of 5%. The Allium cepa test, micronucleus test for human T lymphocytes and erythrocytes of Astyanax sp did not indicate mutagenic and / or genotoxic potential of phytochemicals (p> 0.05) when compared to the non-exposed controls, except the concentration of 5 mg/L of B. gaudichaudii that showed cytotoxicity. On the other hand, the comet assay revealed genotoxic action for all concentrations evaluated for the tail length parameter of the comet. For the moment parameter of Olive's tail only the 20mg /L concentration of Caesalpinia ferrea extract was genotoxic. Therefore, apical meristematic cells from the roots of Allium cepa and human T lymphocytes did not present genotoxic and / or mutagenic changes induced by exposure to both plant extracts detectable by micronuclei tests or mitotic index reduction. Genotoxic effect was evidenced by the tail length and tail moment parameter of Olive in the Comet Assay only for C. ferrea extract in the erythrocytes of Astyanax sp. In order to understand the genotoxic and mutagenic activities of B. gaudichaudii and C. ferrea it is important to increase the number of studies to establish safer doses for human consumption. / As espécies Brosimum gaudichaudii (família Moraceae) e Caesalpinia ferrea da família Fabaceae são amplamente distribuídas pelo território brasileiro e são consideradas plantas medicinais. O extrato das cascas de Brosimum gaudichaudii tem sido indicado para tratamento de mancha de pele e vitiligo. Por outro lado, o extrato dos frutos de Caesalpinia ferrea tem sido usado devido suas propriedades terapêuticas como ação antibacteriana, antiinflamatória e analgésica. A maioria dos fitoquímicos presentes nos extratos de plantas medicinais ainda não foram completamente estudados e podem ser tóxicos para a saúde humana e animal. Nesse sentido, é necessário estudos fitoquímicos qualitativos de metabólitos secundários e avaliação do potencial citotóxico, genotóxico e mutagênico dos extratos destas espécies. Nesse estudo, visando avaliar os efeitos mutagênico e/ou genotóxico, diferentes concentrações das soluções extrativas de B. gaudichaudii e C. ferrea foram avaliadas in vivo em Astyanax sp e em Allium cepa, e em ex vivo, pelo teste de micronúcleos em linfócitos T humanos. Os resultados observados das análises foram submetidos ao teste não paramétrico Kruskall-Wallis e posteriormente a regressão linear simples com nível de significância 5%. O teste em Allium cepa, teste de micronúcleo em linfócitos T humanos e em eritrócitos de Astyanax sp não indicaram potencial mutagênico e/ou genotóxico dos fitoconstituintes (p>0,05) quando comparado aos controles não expostos, exceto a concentração de 5g/L de B. gaudichaudii que apresentou citotoxicidade (p=0,038). Por outro lado, o ensaio cometa, revelou ação genotóxica para todas as concentrações avaliadas no parâmetro comprimento da cauda do cometa, para o parâmetro momento da cauda de Olive, apenas a concentração de 20mg/L do extrato de Caesalpinia ferrea mostrou-se genotóxica. Nenhum dos parâmetros avaliados evidenciou danos genéticos resultantes da exposição aos extratos das cascas do caule de B. gaudichaudii. Portanto, as células meristemáticas apicais das raízes de Allium cepa e os linfócitos T humanos não apresentaram alterações genotóxicas e/ou mutagênicas induzidas pela exposição a ambos extratos vegetais que pudesse ser detectadas pelos testes do micronúcleos ou redução do índice mitóticos. Enquanto, nos eritrócitos de Astyanax sp foi evidenciado ação genotóxica pelo parâmetro comprimento da cauda do cometa e momento de da cauda de Olive somente para o extrato de C. ferrea. Diante do exposto, há necessidade de ampliar os estudos para melhor compreensão das atividades genotóxicas e/ou mutagênicas dos extratos de B. gaudichaudii e C. ferrea visando o estabelecimento de doses mais seguras para o consumo humano.

Thesis. 1978. Ph.D.--Massachusetts Institute of Technology. Dept. of Electrical Engineering and Computer Science. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND ENGINEERING. / Includes bibliographical references. / Ph.D.

High throughput technologies and statistical analyses have transformed the way biological research is performed. These technologies accomplish tasks that were labeled as science fiction only 20 years ago - identifying millions of genetic variations in a genome, a chip that measures expression levels of all genes, quantifying the concentration of dozens of proteins at a single cell resolution. High-throughput genome-wide approaches allowed us, for the first time, to perform unbiased research that doesn't depend on existing knowledge. Thanks to these new technologies, we now have a much better understanding on what goes awry in cancer, what are the genetic predispositions for numerous diseases, and how to select the best available treatment for each patient based on his/her genetic and genomic features. The emergence of new technologies, however, also introduced many new problems that need to be addressed in order to fully exploit the information within the data. Tasks start with data normalization and artifact identification, continue with how to properly model the data using statistical tools, and end with the suitable ways to translate those statistical results into informative and correct biological insights. A new field - computational biology - was emerged to address those problems and bridge the gap between statistics and biology. Here I present 3 studies on computational modeling of heterogeneity and context-specificity in biological systems. My work focused on the identification of genomic features that can predict or explain a phenotype. In my studies of both yeast and cancer, I found vast heterogeneity between individuals that hampers the prediction power of many statistical models. I developed novel computational models that account for the heterogeneity and discovered that, in most cases, the relationship between the genomic feature and the phenotype is context-specific - genomic features explain, predict or exert influence on the phenotype in only a subset of cases. In the first project I studied the landscape of genetic interactions in yeast using gene expression data. I found that roughly 80% of interactions are context-specific, where genetic mutations influence expression levels only in the context of other mutations. In the second project I used gene expression and copy number data to identify drivers of oncogenesis. By using gene expression as a phenotype, and by accounting for context-specificity, I identified two novel copy number drivers that were validated experimentally. In the third project I studied the transcriptional and phenotypic effects of MAPK pathway inhibition in melanoma. I show that most MAPK targets are context-specific - under the control of the pathway only in a subset of cell lines. A computational model I designed to detect context-specific interactions of the MAPK pathway identified the interferon pathway as a major player in the cytotoxic response of MAPK inhibition. Taken together, my research demonstrates the importance of context-specificity in the analysis of biological systems. Context-specific computational modeling, combined with high-throughput technologies, is a powerful tool for dissecting biological networks.

Cichlid fishes from the East African Rift lakes Victoria, Tanganyika and Malawi represent a preeminent example of replicated and rapid evolutionary radiation. In this single natural system, numerous morphological (eg. jaw and tooth shape, color patterns, visual sensitivity), behavioral (eg. bower-building) and physiological (eg. development, neural patterning) phenotypes have emerged, much akin to a mutagenic screen. This dissertation encompasses three studies that seek to decipher the underpinnings of such rapid evolutionary diversification, investigated via the genetic variation in East African cichlids. We generated a valuable cichlid genomic resource of five low-coverage Lake Malawi cichlid genomes, from which the general properties of the genome were characterized. Nucleotide diversity of Malawi cichlids was low at 0.26%, and a sample genotyping study found that biallelic polymorphisms segregate widely throughout the Malawi species flock, making each species a mosaic of ancestrally polymorphic genomes. A second genotyping study expanded our evolutionary analysis to cover the entire East African cichlid radiation, where we found that more than 40% of single nucleotide polymorphisms (SNPs) were ancestral polymorphisms shared across multiple lakes. Bayesian analysis of genetic structure in the data supported the hypothesis that riverine species had contributed significantly to the genomes of Malawi cichlids and that Lake Malawi cichlids are not monophyletic. Both genotyping studies also identified interesting loci involved in important sensory as well as developmental pathways that were well differentiated between species and lineages. We also investigated cichlid genetic variation in relation to the evolution of microRNA regulation, and found that divergent selection on miRNA target sites may have led to differential gene expression, which contributed to the diversification of cichlid species. Overall, the patterns of cichlid genetic variation seem to be dominated by the phenomena of extensive sharing of ancestral polymorphisms. We thus believe that standing genetic variation in the form of ancestrally inherited polymorphisms, as opposed to variations arising from new mutations, provides much of the genetic diversity on which selection acts, allowing for the rapid and repeated adaptive radiation of East African cichlids.