Department of Bioengineering Faculty Research and Papers

Permanent URI for this collectionhttps://digital.lib.washington.edu/handle/1773/15615

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    Tellurium and libRoadRunner tutorial for the COMBINE & de.NBI 2019 Workshop on Modeling and Simulation Tools in Systems Biology
    (2019-11-19)
    This tutorial guides a user through fifteen modeling challenges together with an introduction to biochemical pathway modeling using the Python/Tellurium package. This tutorial was presented at the COMBINE tutorial at the 20th International Conference on Systems Biology.
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    Class notes on oscillators: Systems and Synthetic Biology
    (2019-11-14) Sauro, Herbert M.
    This is a slide deck for a class on oscillator circuits found in systems and synthetic biology.
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    Internalization of novel non-viral vector TAT-streptavidin into human cells
    (2007) Rinne, Johanna; Albarran, Brian; Jylhävä, Juulia; Ihalainen, Teemu O.; Kankaanpää, Pasi; Hytönen, Vesa P.; Stayton, Patrick S.; Kulomaa, Markku S.; Vihinen-Ranta, Maija
    Background: The cell-penetrating peptide derived from the Human immunodeficiency virus-1 transactivator protein Tat possesses the capacity to promote the effective uptake of various cargo molecules across the plasma membrane in vitro and in vivo. The objective of this study was to characterize the uptake and delivery mechanisms of a novel streptavidin fusion construct, TAT[sub]47-57-streptavidin (TAT-SA, 60 kD). SA represents a potentially useful TAT-fusion partner due to its ability to perform as a versatile intracellular delivery vector for a wide array of biotinylated molecules or cargoes. Results: By confocal and immunoelectron microscopy the majority of internalized TAT-SA was shown to accumulate in perinuclear vesicles in both cancer and non-cancer cell lines. The uptake studies in living cells with various fluorescent endocytic markers and inhibiting agents suggested that TAT-SA is internalized into cells efficiently, using both clathrin-mediated endocytosis and lipidraft- mediated macropinocytosis. When endosomal release of TAT-SA was enhanced through the incorporation of a biotinylated, pH-responsive polymer poly(propylacrylic acid) (PPAA), nuclear localization of TAT-SA and TAT-SA bound to biotin was markedly improved. Additionally, no significant cytotoxicity was detected in the TAT-SA constructs. Conclusion: This study demonstrates that TAT-SA-PPAA is a potential non-viral vector to be utilized in protein therapeutics to deliver biotinylated molecules both into cytoplasm and nucleus of human cells.
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    Biomaterials Approaches to Combating Oral Biofilms and Dental Disease
    (2006) Bryers, James D.; Ratner, Buddy D.
    Background: Possibilities for biomaterials to impact the dental caries epidemic are reviewed with emphasis placed on novel delivery biomaterials and new therapeutic targets.
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    Biotech and Biomaterials Research to Reduce the Caries Epidemic
    (2006) Slayton, Rebecca L.; Bryers, James D.; Milgrom, Peter
    The goal of this workshop is to develop a consensus within the biomaterials/bioengineering community for a research agenda focused on creating technologies that will address the current dental caries pandemic. The workshop will bring together expertise from academia, industry, and the NIH institutes in the areas of oral biofilm microbiology and innovative biomaterials. The rationale for the workshop is that science and technology have not produced sufficient practical tools for public health practitioners and the private delivery system to address the pandemic in dental caries that exists for children and adults from families with low incomes and for numerous ethnic minority and racial groups. Moreover, it is unclear whether the barriers are remediable bioengineering and technical problems or fundamental science questions. Nevertheless, the obligation to address the gap between scientific research and practical application is especially relevant today. The U.S. and state governments bear the majority of the cost of trying to control this pandemic through Medicaid, the Public Health Service, Indian Health Service and other similar programs. These costs continue to escalate as continued applications of existing technology are unlikely to markedly reduce disparities. The mainstays of caries prevention, topical and systemic fluorides and pit and fissure sealants, are technologies developed in the 1950s and 1960s.