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Biochemical and Biomolecular Engineering
The Summer Undergraduate Research Fellowship (SURF) Symposium
- Keyword
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- Hydrogels (2)
- Lignin (2)
- Phenylalanine (2)
- Yeast (2)
- ATP (1)
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- Arabidopsis (1)
- Balance (1)
- Biofuel (1)
- Biomarkers (1)
- Bioreactor (1)
- CRISPR (1)
- Cancer (1)
- Carbon nanotubes (1)
- Cartilage engineering (1)
- Cellulosic biomass (1)
- Chromophore (1)
- Cyanobacteria (1)
- DNA methylation (1)
- Elastin (1)
- Enzyme (1)
- Epigenetics (1)
- Flux balance analysis (1)
- Gene (1)
- Genome scale model (1)
- Group Contribution (1)
- HPLC (1)
- IGEM (1)
- Interfacial Layer (1)
- LC-MS/MS (1)
- Limiting (1)
Articles 1 - 12 of 12
Full-Text Articles in Engineering
Targeted Epigenetic Editing Using Optogenetic Tools, Joshua Hahn, Chongli Yuan
Targeted Epigenetic Editing Using Optogenetic Tools, Joshua Hahn, Chongli Yuan
The Summer Undergraduate Research Fellowship (SURF) Symposium
Epigenetics markers, such as DNA methylation and histone post-translational modifications, are modifications to the structure of DNA that impact gene expression without altering the genetic code. Among them, DNA methylation plays a critical role in various biological processes including the differentiation of stem cells, regulation of gene expression, and adaptation to environmental signals. The ability to modify DNA methylation at particular genes in various cell types is thus desirable for engineering specific cell phenotypes. Although technologies exist that can alter DNA methylation at target genes, these techniques lack spatial and temporal resolution and are not able to selectively edit individual …
Thermodynamic Analysis Of Phenylpropanoid Pathway In Arabidopsis Thanliana, Patrick J. Ioerger, Rohit Jaini, John A. Morgan
Thermodynamic Analysis Of Phenylpropanoid Pathway In Arabidopsis Thanliana, Patrick J. Ioerger, Rohit Jaini, John A. Morgan
The Summer Undergraduate Research Fellowship (SURF) Symposium
Biofuels represent a renewable alternative to traditional fossil fuels. As dependence on fossil fuels rise so does the importance of improving the production of alternative fuels. Lignin poses one obstacle in the development of such alternative fuels. Its presence strengthens cell walls and hinders degradation of polysaccharides into monosaccharides, increasing cost and time while decreasing efficiency of the process. Lignin is composed of three monolignols, each of which is produced through the Phenylpropanoid pathway; a series of chemical reactions. This work aims to determine which reactions in the pathway are least thermodynamically favorable and thus most limiting. From metabolic mapping …
Development Of A Novel Enzymatic Pre-Treatment For Lignocellulosic Biomass, Melissa Robins, Jenna Rickus
Development Of A Novel Enzymatic Pre-Treatment For Lignocellulosic Biomass, Melissa Robins, Jenna Rickus
The Summer Undergraduate Research Fellowship (SURF) Symposium
Biofuels, fuels derived directly from living matter, present a renewable and environmentally friendly alternative to petroleum based fuels. Bioethanol produced from low input energy crops or agricultural waste is a promising fuel source because it does not interfere with the human food supply chain and the ethanol produced can be blended with gasoline. These potential sources of bioethanol are not yet commercially viable due to a polymer called lignin present in the plant’s cell wall which impedes the conversion of cellulose to glucose and the eventual fermentation of glucose to ethanol. Developing new methods for the pretreatment of lignocellulosic biomass …
The Identification Of Optimal Pathways In Synechocystis Sp. Pcc 6803 By Flux Balance Analysis, Ning Xuan Yip, John A. Morgan, Longyun Guo
The Identification Of Optimal Pathways In Synechocystis Sp. Pcc 6803 By Flux Balance Analysis, Ning Xuan Yip, John A. Morgan, Longyun Guo
The Summer Undergraduate Research Fellowship (SURF) Symposium
Cyanobacteria are microorganisms considered advantageous for producing valuable compounds because of their high growth rates compared to plants. They also can be grown at large scale in photobioreactors. This research aims to use metabolic engineering strategies to maximize the phenylalanine yield in Synechocystis sp. PCC 6803. Our hypothesis is flux balance analysis will give different flux distributions with different objective functions. The scope of the project is modeling photoautotrophic metabolism of cyanobacteria with a genome scale stoichiometric model, testing several alternative objective functions. We also examined the tradeoff between growth and L-phenylalanine production with flux balance analysis. A linear programming …
A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus
A Novel Synthetic Yeast For Enzymatic Biodigester Pretreatment, Tianyu Tan, Mark S. Aronson, Arren Liu, Jill H. Osterhus, Melissa Robins, Suraj Mohan, Erich Leazer, Bowman Clark, Alexa Petrucciani, Katherine Lowery, James Welch, Casey Martin, Helena Lysandrou, Michael E. Scharf, Jenna Rickus
The Summer Undergraduate Research Fellowship (SURF) Symposium
Lignin, a complex organic polymer, is a major roadblock to the efficiency of biofuel conversion as it both physically blocks carbohydrate substrates and poisons biomass degrading enzymes, even if broken down to monomer units. A pretreatment process is often applied to separate the lignin from biomass prior to biofuel conversion. However, contemporary methods of pretreatment require large amounts of energy, which may be economically uncompelling or unfeasible. Taking inspiration from several genes that have been isolated from termites and fungi which translate to enzymes that degrade lignin, we want to establish a novel “enzymatic pretreatment” system where microbes secrete these …
Characterization Of Swelling Ratio And Water Content Of Hydrogels For Cartilage Engineering Applications, Emily E. Gill, Renay S.-C. Su, Julie C. Liu
Characterization Of Swelling Ratio And Water Content Of Hydrogels For Cartilage Engineering Applications, Emily E. Gill, Renay S.-C. Su, Julie C. Liu
The Summer Undergraduate Research Fellowship (SURF) Symposium
Due to the high prevalence of arthritis and cartilage-related injuries, tissue engineers are studying ways to grow cartilage tissue replacements. Resilin, an elastomeric protein found in insect cuticles, is known for its extraordinary resilience and elasticity. In previous studies, recombinant resilin-based hydrogels, or cross-linked protein networks, exhibited potential for use in cartilage tissue scaffolds. Our lab successfully developed resilin-based proteins with a sequence based on the mosquito gene and showed that resilin-based hydrogels possess mechanical properties of the same order of magnitude as native articular cartilage. In addition, these mechanical properties can be controlled by changing the protein concentration. To …
Population Balance Modeling Of Conjugation In Enterococcus Faecalis, Jeremy Binagia, Vu Tran, Che-Chi Shu, Doraiswami Ramkrishna
Population Balance Modeling Of Conjugation In Enterococcus Faecalis, Jeremy Binagia, Vu Tran, Che-Chi Shu, Doraiswami Ramkrishna
The Summer Undergraduate Research Fellowship (SURF) Symposium
In the bacteria species Enterococcus faecalis, transfer of plasmid pCF10 by conjugation between donor cells that possess sets of genes conferring drug resistance and recipient cells leads to the spread of this resistance in a population. A complex signaling molecule network is responsible for communication between recipient and donor cells. Up to this point, the nature of these signaling molecules has been modeled deterministically from the point of view of an “average” cell. While this view has been cured slightly by stochastic treatments, a model is needed that better accounts for the individual nature of each cell, each cell’s interactions …
Dna Based Carbon Nanotube Porphyrin Nanohybrids Molecular Recognization And Regeneration, Molly M. Riccitelli, Hanyu Zhang, Jong Hyun Choi
Dna Based Carbon Nanotube Porphyrin Nanohybrids Molecular Recognization And Regeneration, Molly M. Riccitelli, Hanyu Zhang, Jong Hyun Choi
The Summer Undergraduate Research Fellowship (SURF) Symposium
In the search to improve solar cells, scientists are exploring new materials that will provide better current transfer. One material that has emerged as a strong contender is the single walled carbon nanotube (SWNT). Current DNA-SWNT based films combined with chromophores have poor operational lifetimes compared to commercial solar cells. Once exposed to light the chromophore begins to degrade, eventually rendering the solar cell unusable. To solve this problem, we used a method involving multiple steps. First we found which DNA sequences formed structures around the SWNT that could hold the most chromophores by using a spectrophotometer to test the …
Multi-Factorial Stability Study Of Metabolites, Ruijun Zheng, John A. Morgan
Multi-Factorial Stability Study Of Metabolites, Ruijun Zheng, John A. Morgan
The Summer Undergraduate Research Fellowship (SURF) Symposium
Previous research done on metabolites has found that high energy compounds like adenosine triphosphate(ATP), nicotinamide adenine dinucleotide phosphate reduced (NADPH) or nicotinamide adenine dinucleotide reduced (NADH) are unstable in cell extracts at relatively high temperature and acidic condition. The multifactorial stability study of metabolites enables us to verify the best condition of storage for these energy compounds and sugar phosphates, as well as to strengthen the understanding of metabolism in biological study. As the most solvents for high performance liquid chromatography (HPLC) are acidic and unfavorable for these energy compounds, it is necessary to perform a detailed study about …
Tobacco Mosaic Virus Implemented As An Interfacial Layer In Organic Photovoltaic Cells, Monica D. Del Real, Bryan Boudouris
Tobacco Mosaic Virus Implemented As An Interfacial Layer In Organic Photovoltaic Cells, Monica D. Del Real, Bryan Boudouris
The Summer Undergraduate Research Fellowship (SURF) Symposium
Organic photovoltaics (OPVs) are flexible, light weight, and economical to produce due to low processing temperatures, solution processing, and print fabrication. This makes them optimal for a wide range of applications. However, the efficiencies of OPVs are currently not high enough for them to be viable in the market or to be able to compete with inorganic photovoltaics. Therefore the integration of new materials and methods into OPVs in order to increase their efficiency is a vital field. One way to increase the efficiency of OPVs is to increase the surface area in-between layers to allow for enhanced electron transport. …
Biomarkers For Vincristine-Induced Neuropathy, Danni Li, Jayachandran Devaraj, Doraiswami Ramkrishna
Biomarkers For Vincristine-Induced Neuropathy, Danni Li, Jayachandran Devaraj, Doraiswami Ramkrishna
The Summer Undergraduate Research Fellowship (SURF) Symposium
Vincristine is a vinca alkaloid, a commonly used chemotherapy drug for treating leukemia, lymphoma, multiple myeloma and some pediatric cancers. Its major dose-limiting side effect is peripheral neuropathy. The current dosing of “standard-dose-for-all” ignores the genetic and phenotypic variations among different patients, and causes severe neuropathy in some patients while ineffectively treats the others. In the present study, we aim to discover novel biomarkers involved in vincristine-induced neuropathy and identify patients with varied metabolic characteristics. Thus treatment can be tailored accordingly to improve outcomes of vincristine treatment. Pre-dose and post-dose serum samples were collected from two groups of patients (low …
Adhesive Elastomeric Proteins, Haefa Mansour, Julie Liu
Adhesive Elastomeric Proteins, Haefa Mansour, Julie Liu
The Summer Undergraduate Research Fellowship (SURF) Symposium
Sutures and staples commonly used to close surgical wounds tend to be much stiffer than the surrounding tissue, often resulting in external tissue damage. Surgical adhesives provide a promising alternative to these sutures and staples. Ideal surgical adhesives are biocompatible, able to set well and remain sticky in moist conditions, possess strong adhesive and cohesive properties, and exhibit mechanical properties that mimic those of the surrounding tissue. Unfortunately, the adhesives available today are unable to satisfactorily meet all of these criteria. We are utilizing protein engineering techniques to design, create, and test a new surgical adhesive that combines the adhesive …