Thesis (Ph. D.)--Ohio State University, 2006. / Title from first page of PDF file. Includes bibliographical references (p. 140-154).

Thesis (Ph. D. in Biochemistry)--Vanderbilt University, Dec. 2007. / Title from title screen. Includes bibliographical references.

Jena, Univ., Diss., 2005

Techn. Hochsch., Diss., 2005--Aachen.

Thesis (Ph. D.)--University of Texas at Austin, 2008. / Vita. Includes bibliographical references.

Kyoto University (京都大学) / 0048 / 新制・課程博士 / 博士(工学) / 甲第15407号 / 工博第3286号 / 新制||工||1495(附属図書館) / 27885 / 京都大学大学院工学研究科合成・生物化学専攻 / (主査)教授 濵地 格, 教授 森 泰生, 教授 白川 昌宏 / 学位規則第4条第1項該当

Regional and global trends in aquaculture production, value and price are assessed for the last 30 years relative to trends in wild caught species. Based on data from the Fisheries and Aquaculture Department of the Food and Agriculture Organization of the United Nations for aquaculture production, data is extracted for the first time to address regional (Europe, North America, South America, Africa, Oceania and Asia) trends in production focused on the top five aquaculture produced species. Previous uses of the database have largely focused on global production. Of the top five species (whiteleg shrimp Penaeus vannamei, Atlantic salmon Salmo salar, silver carp Hypophthalmichthys molitrix, common carp Cyprinus carpio, and giant tiger prawn Penaeus monodon), Asia accounts for most of the global production (with the exception of Atlantic salmon Salmo salar). The central issue considered in this thesis concerns the likelihood and capacity of aquaculture production of fish and shellfish protein for human consumption relative to that of exploited wild stocks. Over the last 30 years or so, aquaculture production has risen exponentially and captures of wild caught fish have now plateaued. The relative status, rearing practices, production and basic economic perspectives of the principle aquaculture produced species globally are compared with wild caught production. The principle finding is that total global aquaculture production will exceed that of commercial wild caught species by about 2015. The significance of this is discussed in terms of current views of environmental (e.g. pollution, disease and habitat degradation) and economic (e.g. production level, farm price, marketing economics, fixed costs (facility and equipment depreciation, loan interest, land lease, fixed wages), variable costs (cost of seed stock, feed, energy)) impacts of aquaculture. Similarly, these issues are considered for the fishing industry (e.g. fishing down the food web, likelihood of expansion of bottom fisheries into deeper waters, reduction of biodiversity, declining global catches). It is concluded that aquaculture is a necessity and that if current trends continue aquaculture production can more than supplement human fish protein needs even in the given context of the rapid growing population, but that in the long term aquaculture production will itself be substantially supplemented by “rebounding” wild fishery production. / Science, Faculty of / Resources, Environment and Sustainability (IRES), Institute for / Graduate

Protein-protein interactions modulate cellular processes in health and disease. However, tracing weak or rare associations or dissociations of proteins is not a trivial task. Kinases are often regulated through interaction partners and, at the same time, themselves regulate cellular interaction networks. The use of kinase domains for creating a synthetic sensor device that reads low concentration protein-protein interactions and amplifies them to a higher concentration interaction which is then translated into a FRET (Fluorescence Resonance Energy Transfer) signal is here proposed. To this end, DNA constructs for interaction amplification (split kinases), positive controls (intact kinase domains), scaffolding proteins and phosphopeptide - SH2-domain modules for the reading of kinase activity were assembled and expression protocols for fusion proteins containing Lyn, Src, and Fak kinase domains in bacterial and in cell-free systems were optimized. Also, two non-overlapping methods for measuring the kinase activity of these proteins were stablished and, finally, a protein-fragment complementation assay with the split-kinase constructs was tested. In conclusion, it has been demonstrated that features such as codon optimization, vector design and expression conditions have an impact on the expression yield and activity of kinase-based proteins. Furthermore, it has been found that the defined PURE cell-free system is insufficient for the active expression of catalytic kinase domains. In contrast, the bacterial co-expression with phosphatases produced active kinase fusion proteins for two out of the three tested Tyrosine kinase domains.

The number of available protein sequences in public databases is increasing exponentially. However, a significant fraction of these sequences lack functional annotation which is essential to our understanding of how biological systems and processes operate. In this master thesis project, we worked on inferring protein functions based on the primary protein sequence. In the approach we follow, 3D models are first constructed using I-TASSER. Functions are then deduced by structurally matching these predicted models, using global and local similarities, through three independent enzyme commission (EC) and gene ontology (GO) function libraries. The method was tested on 250 “hard” proteins, which lack homologous templates in both structure and function libraries. The results show that this method outperforms the conventional prediction methods based on sequence similarity or threading. Additionally, our method could be improved even further by incorporating protein-protein interaction information. Overall, the method we use provides an efficient approach for automated functional annotation of non-homologous proteins, starting from their sequence.

Late SV40 factor (LSF) is a CP2 family transcription factor involved in cell cycle regulation. In liver cancer, LSF is an oncogene, in part due to its role in upregulation of osteopontin leading to increase tumor size. As a result, LSF is a potential target for drug discovery. LSF binds the p65 subunit of the transcription factor NFkB and also the transcription factor ying yang 1 (YY1). In this thesis, I show that binding of both YY1 and p65 occurs at the ubiquitin-like domain of LSF in U2OS cell extracts. Interestingly, when phosphatase inhibitors are added during preparation of U2OS cell extracts, the binding of YY1 and p65 to LSF shifts from the ubiquitin-like domain of LSF to the DNA binding domain. The role of a yet unidentified docking protein may be responsible for this shift in binding. In an attempt to map the specific region of the LSF sequence that is involved in these interactions, I have developed a peptide identification assay which utilizes protease digestion, protein mediated peptide capture, and LC ESI-MS. Through the use of this assay, I'm confident that the sequence(s) involved in these LSF protein-protein interactions can be further defined.