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Currently there are approximately 20,000 valid gene patents in the United States. The debate regarding biotechnology and patent law has reached a pinnacle over the patentability of genes. Biotech is fighting a patentability war on two fronts. The Court of Appeals for the Federal Circuit cannot agree regarding the touchstone of patentability for genes; two branches of the Executive are at odds over whether gene sequences qualify under 35 U.S.C. §101. Recent U.S. Supreme Court and Federal Circuit jurisprudence also undermine the patentability of genes as obvious. This thesis argues that the patentable subject matter debate fails to adequately address the goals of patent policy in fostering innovation. Looking to Canadian and U.K. jurisprudence, it is possible to hone an approach to obviousness that addresses the ethical and research concerns in the patentable subject matter debate while fostering investment and patent protection for non-obvious biotech discoveries.

<p>The Wingless (Wg)/Wnt signal transduction pathway directs a variety of cell fate decisions in developing animal embryos. Despite the identification of many Wg pathway components to date, it is still not clear how these proteins work together to generate cellular identities. We have carried out a series of genetic screens in Drosophila to identify new components involved in Wg signaling. Two mutant lines that modify wg-mediated epidermal patterning carry mutations in the RacGap50C gene. These mutations on their own cause cuticle pattern disruptions that include replacement of ventral denticles with naked cuticle, which indicate that the Wg pathway is ectopically activated in mutant embryos. In addition, RacGap50C mutations also interact genetically with naked cuticle and Axin, known negative regulators of the Wg pathway. These phenotypes suggest that the RacGap50C gene product participates in the negative regulation of Wg pathway activity. </p><p>In addition to the role of RacGap50C in regulating Wg signaling, RacGap50C, with the kinesin like protein Pavarotti (Pav), is essential for cytokinesis in dividing cells. Surprisingly, Pav, like RacGap50C is able to repress Wnt stimulated reporter gene activity in mammalian tissue culture. Expression of RacGap50C or Pav does not alter the levels of endogenous BetaCatenin, nor does it prevent BetaCatenin from entering the nucleus and binding the transcription factor TCF. However, reporter gene activity is significantly diminished in cells expressing RacGap50C or Pav, indicating an inability of this nuclear BetaCatenin to activate transcription. RacGap50C and Pav are also found in the nucleus of interphase cells and this subcellular localization may be relevant to their role in regulation of the Wnt pathway. Although RacGap50C and Pav colocalize, our data indicate distinct roles for these two proteins in Wnt signaling, as they show different genetic interactions with nkd in Drosophila embryos and with TCF in mammalian cells. </p><p>In addition, I have identified regions of the RacGap50C proteins that are dispensable for Wnt signaling repression. Pav-binding region, and the cysteine rich region of RacGap50C are not required for the activity of RacGap50C in Drosophila embryos, nor is GAP activity. Conversely, the middle region of the RacGap50C, which contains a nuclear localization signal, and the RacGap domain, which contains regions required for cofactor binding, are required for RacGap50C regulation of Wnt signaling. In summary, these results indicate a unique role for RacGap50C and Pav in regulating Wnt signaling at the level of BetaCatenin target gene activation.</p> / Dissertation

<p>The physiology of the tumor microenvironment is characterized by lower oxygen (hypoxia), higher lactate, extracellular acidosis and glucose starvation. We examined the global, transcriptional cellular responses to each of these microenvironmental stresses in vitro, projected them onto clinical breast cancer patients' samples in vivo, and returned to perform further in vitro experiments to investigate the potential mechanisms involved in these stress responses. The reciprocal exchange of information was critical and advanced our understanding of the potential clinical relevance of cellular responses. </p> <p>Our expression array result showed that lactic acidosis induces a strong response, distinct from that of hypoxia in human mammalian epithelial cells (HMECs), indicating lactic acidosis is not only a by-product of hypoxia but has a unique role as a stimulant to cells in the tumor microenvironment. Cellular responses to lactosis and acidosis further demonstrated that acidosis was the main driving force in the lactic acidosis response. These responding gene signatures were then statistically projected into clinical breast cancer patients' expression data sets. The hypoxia response, as reported previously, was associated with bad prognosis, where as the lactic acidosis and acidosis responses, were associated with good prognosis. Additionally, the acidosis response could be used to separate breast tumors with high versus low aggressiveness based on its inversed correlation with metastatic character. We further discovered that lactic acidosis, in contrast to hypoxia, abolished Akt signaling. Moreover, it downregulated glycolysis and shifted energy utilization towards aerobic respiration.</p> <p>We continued to examine the cellular response to lactic acidosis temporally in MCF7 cells, a breast cancer cell line. The lactic acidosis response of MCF7 cells also showed the prognostic result of better clinical outcomes in datasets of breast cancer patients. The lactic acidosis responses of HMEC and MCF cells were highly correlated. Strikingly in MCF7 cells, lactic acidosis and glucose deprivation actually induced similar transcriptional profiles, with only a few genes being oppositely regulated. Furthermore, lactic acidosis, similar to glucose starvation, induced AMPK signaling and abolished mTOR. However, lactic acidosis and glucose deprivation induced opposite glucose uptake phenotypes. Lactic acidosis significantly repressed glucose uptake whereas glucose deprivation significantly induced it. Among the genes differentially regulated by these two stresses, thioredoxin-interacting protein (TXNIP) was among the most different. The negative regulatory role of TXNIP on glucose uptake has been demonstrated previously. In the cancer research field, TXNIP is recognized as a tumor suppressor gene. We observed that lactic acidosis induced TXNIP strongly and most importantly, TXNIP played a critical role in regulating glucose uptake in cells under lactic acidosis. Furthermore, MondoA, the transcription factor and glucose sensor previously reported to regulate TXNIP induction upon glucose exposure, was also responsible for regulating TXNIP under lactic acidosis. We demonstrated that TXNIP not only plays an important role in the lactic acidosis response but also has strong prognostic power to separate breast cancer patients based on survival.</p> / Dissertation

Thesis (Ph.D.)--University of California, San Francisco, 2009. / Source: Dissertation Abstracts International, Volume: 70-04, Section: B, page: 2039. Adviser: Didier Y.R. Stainier.

One of the central questions in population genetics is how different forces of evolution influence patterns of genetic variation within and between species. Locus-specific forces of natural selection, like selective sweeps and background selection, are expected to influence only the target of selection and any sites linked to that target. In contrast, genome-wide forces are expected to influence mane different loci simultaneously. In particular, genome-wide forces that have a sex-specific component are predicted to exert disparate influence over the four different genomic compartment, (mitochondrial DNA, non-recombining portion of the Y chromosome (NRY), X chromosome, autosomes) depending on their degree of maternal or paternal inheritance. This study compared levels of genetic variation across the four genomic compartments in the Hominoidea (humans, chimpanzees, bonobos, gorillas, and orangutans) in order to test the hypothesis that a high variance in male reproductive success, as predicted from behavioral data, may influence levels of hominoid genetic diversity. First, comparative chromosome and mitochondria) DNA diversity was quantified across species. NRY diversity was lower than mitochondria) DNA diversity in all taxa, and gorillas exhibited no NRY genetic diversity, consistent with their polygynous mating system. In order to determine whether locus-specific or genome-wide factors were responsible, diversity from all four genomic compartments was compared across species. The multilocus approach revealed patterns of variation across all hominoids that are consistent with a model of high variance in male reproductive success: relatively high mitochondrial DNA diversity, relatively low Y chromosome diversity, and intermediate X and autosomal diversity. Examination of orangutan population structure for NRY, mitochondrial DNA, and X-linked loci suggested an influence of sex-specific demographic influence, but was unclear whether other factors were involved. The study suggests that there is an influence of a high variance in male reproductive success on the hominoid genome, but does not preclude the influence of additional locus-specific factors. There are potentially important implications for population genetic models that assume a sex ratio of 1. Additional loci and additional species need to be examined to determine the generality of the pattern, as well as to further investigate the interplay between genome-wide and locus-specific factors.

Europe is a region characterized by a long history of both settlement and resettlement. This study uses information from the haploid systems of the human genome in order to investigate the presence of population structure in Europe and discuss the mitigating effects of shared population history and the impact of evolutionary forces. By means of two kinds of data from the Y chromosome, the study first establishes patterns of diversity across the entirety of Europe. More in-depth analyses investigate the evolutionary effects of settlement and colonization on overall genetic diversity of populations. Finally, considering data from the entire control region sequence, an effort is made to estimate patterns of mitochondrial diversity and compare their import to that of the Y chromosome.