Matching Items (19)
Filtering by
- Creators: School of Life Sciences
- Creators: Chemical Engineering Program
Description
The impact of physical/chemical properties of gray water on microbial inactivation in gray water using chlorine was investigated through creating artificial gray water in lab, varying specific components, and then measuring microbial inactivation. Gray water was made through taking autoclaved nanopure water, and increasing the concentration of surfacants, the turbidity, the concentration of organic content, and spiking E. coli grown in tryptic soy broth (TSB); chlorine was introduced using Clorox Disinfecting Bleach2. Bacteria was detected using tryptic soy agar (TSA), and E. coli was specifically detected using the selective media, brilliance. The log inactivation of bacteria detected using TSA was shown to be inversely related to the turbidity of the solution. Complete inactivation of E. coli concentrations between 104-105 CFU/100 ml in gray water with turbidities between 10-100 NTU, 0.1-0.5 mg/L of humic acid, and 0.1 ml of Dawn Ultra, was shown to occur, as detected by brilliance, at chlorine concentrations of 1-2 mg/L within 30 seconds. These result in concentration time (CT) values between 0.5-1 mg/L·min. Under the same gray water conditions, and an E. coli concentration of 104 CFU/100 ml and a chlorine concentration of 0.01 mg/L, complete inactivation was shown to occur in all trials within two minutes. These result in CT values ranging from 0.005 to 0.02. The turbidity and humic acid concentration were shown to be inversely related to the log inactivation and directly related to the CT value. This study shows that chlorination is a valid method of treatment of gray water for certain irrigation reuses.
ContributorsGreenberg, Samuel Gabe (Author) / Abbaszadegan, Morteza (Thesis director) / Schoepf, Jared (Committee member) / Alum, Absar (Committee member) / Chemical Engineering Program (Contributor, Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
Nucleic acids encode the information required to create life, and polymerases are the gatekeepers charged with maintaining the storage and flow of this genetic information. Synthetic biologists utilize this universal property to modify organisms and other systems to create unique traits or improve the function of others. One of the many realms in synthetic biology involves the study of biopolymers that do not exist naturally, which is known as xenobiology. Although life depends on two biopolymers for genetic storage, it may be possible that alternative molecules (xenonucleic acids – XNAs), could be used in their place in either a living or non-living system. However, implementation of an XNA based system requires the development of polymerases that can encode and decode information stored in these artificial polymers. A strategy called directed evolution is used to modify or alter the function of a protein of interest, but identifying mutations that can modify polymerase function is made problematic by their size and overall complexity. To reduce the amount of sequence space that needs to be samples when attempting to identify polymerase variants, we can try to make informed decisions about which amino acid residues may have functional roles in catalysis. An analysis of Family B polymerases has shown that residues which are involved in substrate specificity are often highly conserved both at the sequence and structure level. In order to validate the hypothesis that a strong correlation exists between structural conservation and catalytic activity, we have selected and mutated residues in the 9°N polymerase using a loss of function mutagenesis strategy based on a computational analysis of several homologues from a diverse range of taxa. Improvement of these models will hopefully lead to quicker identification of loci which are ideal engineering targets.
ContributorsHaeberle, Tyler Matthew (Author) / Chaput, John (Thesis director) / Chen, Julian (Committee member) / Larsen, Andrew (Committee member) / Barrett, The Honors College (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
Currently in synthetic biology only the Las, Lux, and Rhl quorum sensing pathways have been adapted for broad engineering use. Quorum sensing allows a means of cell to cell communication in which a designated sender cell produces quorum sensing molecules that modify gene expression of a designated receiver cell. While useful, these three quorum sensing pathways exhibit a nontrivial level of crosstalk, hindering robust engineering and leading to unexpected effects in a given design. To address the lack of orthogonality among these three quorum sensing pathways, previous scientists have attempted to perform directed evolution on components of the quorum sensing pathway. While a powerful tool, directed evolution is limited by the subspace that is defined by the protein. For this reason, we take an evolutionary biology approach to identify new orthogonal quorum sensing networks and test these networks for cross-talk with currently-used networks. By charting characteristics of acyl homoserine lactone (AHL) molecules used across quorum sensing pathways in nature, we have identified favorable candidate pathways likely to display orthogonality. These include Aub, Bja, Bra, Cer, Esa, Las, Lux, Rhl, Rpa, and Sin, which we have begun constructing and testing. Our synthetic circuits express GFP in response to a quorum sensing molecule, allowing quantitative measurement of orthogonality between pairs. By determining orthogonal quorum sensing pairs, we hope to identify and adapt novel quorum sensing pathways for robust use in higher-order genetic circuits.
ContributorsMuller, Ryan (Author) / Haynes, Karmella (Thesis director) / Wang, Xiao (Committee member) / Barrett, The Honors College (Contributor) / School of Mathematical and Statistical Sciences (Contributor) / Department of Chemistry and Biochemistry (Contributor) / School of Life Sciences (Contributor)
Created2015-05
Description
One of the primary bottlenecks to chemical production in biological organisms is the toxicity of the chemical. Overexpression of efflux pumps has been shown to increase tolerance to aromatic compounds such as styrene and styrene oxide. Tight control of pump expression is necessary to maximize titers and prevent excessive strain on the cells. This study aimed to identify aromatic-sensitive native promoters and heterologous biosensors for construction of closed-loop control of efflux pump expression in E. coli. Using a promoter library constructed by Zaslaver et al., activation was measured through GFP output. Promoters were evaluated for their sensitivity to the addition of one of four aromatic compounds, their "leaking" of signal, and their induction threshold. Out of 43 targeted promoters, 4 promoters (cmr, mdtG, yahN, yajR) for styrene oxide, 2 promoters (mdtG, yahN) for styrene, 0 promoters for 2-phenylethanol, and 1 promoter for phenol (pheP) were identified as ideal control elements in aromatic bioproduction. In addition, a series of three biosensors (NahR, XylS, DmpR) known to be inducible by other aromatics were screened against styrene oxide, 2-phenylethanol, and phenol. The targeted application of these biosensors is aromatic-induced activation of linked efflux pumps. All three biosensors responded strongly in the presence of styrene oxide and 2-phenylethanol, with minor activation in the presence of phenol. Bioproduction of aromatics continues to gain traction in the biotechnology industry, and the continued discovery of aromatic-inducible elements will be essential to effective pathway control.
ContributorsXu, Jimmy (Author) / Nielsen, David (Thesis director) / Wang, Xuan (Committee member) / School of Life Sciences (Contributor) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
The ability to edit chromosomal regions is an important tool for the study of gene function and the ability to engineer synthetic gene networks. CRISPR-Cas systems, a bacterial RNA-guided immune system against foreign nucleic acids, have recently been engineered for a plethora of genome engineering and transcriptional regulation applications. Here we employ engineered variants of CRISPR systems in proof-of-principle experiments demonstrating the ability of CRISPR-Cas derived single-DNA-strand cutting enzymes (nickases) to direct host-cell genomic recombination. E.coli is generally regarded as a poorly recombinogenic host with double-stranded DNA breaks being highly lethal. However, CRISPR-guided nickase systems can be easily programmed to make very precise, non-lethal, incisions in genomic regions directing both single reporter gene and larger-scale recombination events deleting up to 36 genes. Genome integrated repetitive elements of variable sizes can be employed as sites for CRISPR induced recombination. We project that single-stranded based editing methodologies can be employed alongside preexisting genome engineering techniques to assist and expedite metabolic engineering and minimalized genome research.
ContributorsStandage-Beier, Kylie S (Author) / Wang, Xiao (Thesis director) / Haynes, Karmella (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2014-05
Description
In this research, construction of a model membrane system using Polyvinylidene Chloride-Co Acrylonitrile and Linde Type A zeolites is described. The systems aims to separate out flow through zeolite pores and flow through interfaces between zeolites and polymers through the use of pore filled and pore open zeolites. Permeation tests and salt rejection tests were performed, and the data analyzed to yield approximation of separated flow through zeolites and interfaces. This work concludes the more work is required to bring the model system into a functioning state. New polymer selections and new techniques to produce the membrane system are described for future work.
ContributorsShabilla, Andrew Daniel (Author) / Lind, Mary Laura (Thesis director) / Lin, Jerry (Committee member) / Barrett, The Honors College (Contributor) / Chemical Engineering Program (Contributor)
Created2014-05
Description
This thesis aims to evaluate how in classroom demonstrations compare to regular education techniques, and how student learning styles affect interest in science and engineering as future fields of study. Science education varies between classrooms, but usually is geared towards lecture and preparation for standardized exams without concern for student interest or enjoyment.5 To discover the effectiveness of demonstrations in these concerns, an in classroom demonstration with a water filtration experiment was accompanied by several modules and followed by a short survey. Hypotheses tested included that students would enjoy the demonstration more than a typical class session, and that of these students, those with more visual or tactile learning styles would identify with science or engineering as a possible major in college. The survey results affirmed the first hypothesis, but disproved the second hypothesis; thus illustrating that demonstrations are enjoyable, and beneficial for sparking or maintaining student interest in science across all types of students.
ContributorsPiper, Jessica Marie (Author) / Lind, Mary Laura (Thesis director) / Montoya-Gonzales, Roxanna (Committee member) / Barrett, The Honors College (Contributor) / School of Sustainability (Contributor) / Chemical Engineering Program (Contributor)
Created2014-05
Description
p-Coumaric acid is used in the food, pharmaceutical, and cosmetic industries due to its versatile properties. While prevalent in nature, harvesting the compound from natural sources is inefficient, requiring large quantities of producing crops and numerous extraction and purification steps. Thus, the large-scale production of the compound is both difficult and costly. This research aims to produce p-coumarate directly from renewable and sustainable glucose using a co-culture of Yeast and E. Coli. Methods used in this study include: designing optimal media for mixed-species microbial growth, genetically engineering both strains to build the production pathway with maximum yield, and analyzing the presence of p-Coumarate and its pathway intermediates using High Performance Liquid Chromatography (HPLC). To date, the results of this project include successful integration of C4H activity into the yeast strain BY4741 ∆FDC1, yielding a strain that completely consumed trans-cinnamate (initial concentration of 50 mg/L) and produced ~56 mg/L p-coumarate, a resting cell assay of the co-culture that produced 0.23 mM p-coumarate from an initial L-Phenylalanine concentration of 1.14 mM, and toxicity tests that confirmed the toxicity of trans-cinnamate to yeast for concentrations above ~50 mg/L. The hope for this project is to create a feasible method for producing p-Coumarate sustainably.
ContributorsJohnson, Kaleigh Lynnae (Author) / Nielsen, David (Thesis director) / Thompson, Brian (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-12
Description
Fresh water is essential to the human population and is an integral component in global economics for its multiple uses, and population growth/development cause concern for the possible exhaustion of the limited supply of freshwater. A combined computational and experimental approach to observe and evaluate pervaporation membrane performance for brackish water recovery was done to assess its efficiency and practicality for real world application. Results from modeling conveyed accuracy to reported parameter values from literature as well as strong dependence of performance on input parameters such as temperature. Experimentation results showed improved performance in flux by 34%-42% with radiative effect and then additional performance improvement (9%-33%) with the photothermal effect from carbon black application. Future work will include improvements to the model to include scaling propensity and energy consumption as well as continued experimentation to assess quality of pervaporation in water recovery.
ContributorsDurbin, Mitchell (Co-author) / Rivers, Frederick (Co-author) / Lind Thomas, MaryLaura (Thesis director) / Durgan, Pinar Cay (Committee member) / Chemical Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Current research into live-cell dynamics, particularly those relating to chromatin structure and remodeling, are limited. The tools that are used to detect state changes in chromatin, such as Chromatin Immunoprecipitation and qPCR, require that the cell be killed off. This limits the ability of researchers to pinpoint changes in live cells over a longer period of time. As such, there is a need for a live-cell sensor that can detect chromatin state changes. The Chromometer is a transgenic chromatin state sensor designed to better understand human cell fate and the chromatin changes that occur. HOXD11.12, a DNA sequence that attracts repressive Polycomb group (PCG) proteins, was placed upstream of a core promoter-driven fluorescent reporter (AmCyan fluorescent protein, CFP) to link chromatin repression to a CFP signal. The transgene was stably inserted at an ectopic site in U2-OS (osteosarcoma) cells. Expression of CFP should reflect the epigenetic state at the HOXD locus, where several genes are regulated by Polycomb to control cell differentiation. U2-OS cells were transfected with the transgene and grown under selective pressure. Twelve colonies were identified as having integrated parts from the transgene into their genomes. PCR testing verified 2 cell lines that contain the complete transgene. Flow cytometry indicated mono-modal and bimodal populations in all transgenic cell colonies. Further research must be done to determine the effectiveness of this device as a sensor for live cell state change detection.
ContributorsBarclay, David (Co-author) / Simper, Jan (Co-author) / Haynes, Karmella (Thesis director) / Brafman, David (Committee member) / School of Life Sciences (Contributor) / Harrington Bioengineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05