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Articles 1 - 24 of 24
Full-Text Articles in Biotechnology
Engineering Bioluminescent Sensors Of Cyclic Amp To Study Opioid Signaling, Alexander L. Tesmer, Alexander R. French, Mathew Tantama
Engineering Bioluminescent Sensors Of Cyclic Amp To Study Opioid Signaling, Alexander L. Tesmer, Alexander R. French, Mathew Tantama
The Summer Undergraduate Research Fellowship (SURF) Symposium
Opioids are small signaling molecules which bind to opioid receptors on the surface of cells. The kappa opioid receptor (KOR) is one of three major types of opioid receptors found in human neurons. When an opioid binds to a KOR, a variety of biochemical signaling pathways are activated inside the cell. Each of these pathways are associated with different physiological effects of KOR activation. The production of a small signaling molecule, cyclic adenosine monophosphate (cAMP), is known to be inhibited during KOR activation of the analgesic (pain-killing) signaling pathway. The ability to interrogate the individual responses of KOR signaling pathways …
Cost-Effective Paper-Based Diagnostic Using Split Proteins To Detect Yeast Infections, Zachary R. Berglund, Kevin V. Solomon, Mohit S. Verma, Moiz Rasheed, Zachary Hartley, Kevin Fitzgerald, Kok Zhi Lee, Janice Chan, Julianne Dejoie, Makayla Schacht, Alex Zavala
Cost-Effective Paper-Based Diagnostic Using Split Proteins To Detect Yeast Infections, Zachary R. Berglund, Kevin V. Solomon, Mohit S. Verma, Moiz Rasheed, Zachary Hartley, Kevin Fitzgerald, Kok Zhi Lee, Janice Chan, Julianne Dejoie, Makayla Schacht, Alex Zavala
The Summer Undergraduate Research Fellowship (SURF) Symposium
The common yeast infection, vulvovaginal candidiasis, affects three out of four women throughout their lifetime and can be spread to their child in the form of oral candidiasis (thrush). This disease is caused by the fungal pathogen Candida albicans, which is also a major cause of systemic candidiasis, a rarer but deadly disease with up to a 49% lethality rate. Current widely-used diagnostic methods include cell cultures, pH tests, and antibody detection, to assist effective treatment. Despite availability of various diagnostic methods, there is no inexpensive, rapid, and accurate way to detect C. albicans infection. This project aims to …
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 …
Genome Analysis Of Multiple Mycobacteriophage, Emily Kerstiens, Kari Clase, Yi Li, Gillian Smith, Sarah Bell
Genome Analysis Of Multiple Mycobacteriophage, Emily Kerstiens, Kari Clase, Yi Li, Gillian Smith, Sarah Bell
The Summer Undergraduate Research Fellowship (SURF) Symposium
Bacteriophage are viruses that infect and kill bacteria. They can be used as treatments for antibiotic resistant bacterial infections, but more knowledge is needed about phage and how they interact with bacteria in order to develop safe and effective phage therapy treatments. This study examines the genomes of eighteen mycobacteriophage that were isolated from the environment on and surrounding Purdue University. Phage genomes were annotated using several bioinformatics software, including DNA Master, GeneMark, and PECAAN. Evidence was examined to determine the correct location within the genome and the potential function. Approximately two thousand genes were annotated in this study. A …
Targeting Neuropeptides To Bone Fractures For Accelerated Healing, Nicholas A. Young, Jeffery J. Nielsen, Philip S. Low
Targeting Neuropeptides To Bone Fractures For Accelerated Healing, Nicholas A. Young, Jeffery J. Nielsen, Philip S. Low
The Summer Undergraduate Research Fellowship (SURF) Symposium
In patients over the age of 65 especially, bone fractures represent a significant disease burden. Non-invasive drug therapies are not available for bone fractures which represents a problem for this population. Vasoactive intestinal peptide (VIP) and Pituitary Adenylate Cyclase-Activating Polypeptide (PACAP), two neuromodulator peptides in the glucagon superfamily, have demonstrated positive regulation of osteoblast proliferation and activity. Using acidic oligopeptides, we have developed ligands that target to and accumulate at fracture sites. These targeting ligands can be synthesized in sequence with bone anabolic peptides to minimize off target effects and increase potency at the fracture site to create safer and …
The Response Of Schwann Cells To Weak Dc Electric Fields, Alexander T. Lai, Jianming Li
The Response Of Schwann Cells To Weak Dc Electric Fields, Alexander T. Lai, Jianming Li
The Summer Undergraduate Research Fellowship (SURF) Symposium
Schwann cells are glial cells that serve the vital role of supporting neurons in the peripheral nervous system. While their primary function is to provide insulation (myelin) for axons, they also help regenerate injured axons by digesting severed axons and providing scaffolding to guide the regeneration process. This specific role of Schwann cells makes them highly important cellular targets following nerve injury. Although some efforts have been made to encourage Schwann cell migration after nerve damage, the use of electric fields to control cell responses remain unexplored; therefore, this experiment serves to characterize the behavior of Schwann cells to weak …
Metabolic Comparison Of Wild-Type And Transgenic Synechocystis Pcc 6803 Cyanobacteria, Ian A. Mcluckey, John A. Morgan, Joel Yu King Hing
Metabolic Comparison Of Wild-Type And Transgenic Synechocystis Pcc 6803 Cyanobacteria, Ian A. Mcluckey, John A. Morgan, Joel Yu King Hing
The Summer Undergraduate Research Fellowship (SURF) Symposium
The Calvin-Benson (CBB) cycle is an essential part of nature. This phenomenon allows carbon molecules in carbon dioxide from the atmosphere to be converted into useful energy in the form of sugars. Cyanobacteria are single-celled organisms capable of utilizing energy from sunlight to drive this cycle and are also readily engineered. In hopes of improving this cycle, we compared a wild-type version of the Synechocystis PCC6803 cyanobacteria to an engineered version overexpressing the enzyme FBA (fructose-biphosphate aldolase), called 70 glpX, to deduce how the overexpressing strain is able to be more photosynthetically efficient. To do this, comparative metabolomics were done …
Fret Biosensors: Engineering Fluorescent Proteins As Biological Tools For Studying Parkinson’S Disease, Nathan J. Leroy, Jacob R. Norley, Saranya Radhakrishnan, Mathew Tantama
Fret Biosensors: Engineering Fluorescent Proteins As Biological Tools For Studying Parkinson’S Disease, Nathan J. Leroy, Jacob R. Norley, Saranya Radhakrishnan, Mathew Tantama
The Summer Undergraduate Research Fellowship (SURF) Symposium
Parkinson’s Disease (PD) is a common neurodegenerative disease with over 200,000 new cases each year. In general, the cause of the disease is unknown, but oxidative stress inside of neurons has been associated with the disease’s pathology for some time. Currently, techniques to study the onset of PD inside of neurons are limited. This makes treatments and causes difficult to discover. One solution to this has been fluorescent protein biosensors. In short, these proteins can be engineered to glow when a certain state is achieved inside a cell. The present research discusses the engineering of a genetically-encoded fluorescent protein (FP) …
Fluorescent Protein Biosensor For Use In Parkinson's Research, Piper R. Miller, Keelan Trull, Mathew Tantama
Fluorescent Protein Biosensor For Use In Parkinson's Research, Piper R. Miller, Keelan Trull, Mathew Tantama
The Summer Undergraduate Research Fellowship (SURF) Symposium
Purinergic signaling is a type of extracellular communication that occurs between cells, mediated by adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine. In Parkinson’s Disease, purinergic signaling is disrupted, which contributes to neurodegeneration. In order to monitor this change in cell-to-cell signaling, there is a need for the development of a fluorescent protein (FP) biosensor to study the changes in the concentration of the signaling molecule ATP and its decomposition bioproduct ADP. This summer a genetically encoded ADP sensor that measures changes in ADP concentration was developed. This sensor utilizes Forster Resonance Energy Transfer (FRET) which is a sensing technique …
Low-Cost Diagnostics: A Novel Aptamer Screening Process, Junkai Xie, Kalie Janece Dicks, Oscar C. Sanchez-Medina, Chongli Yuan
Low-Cost Diagnostics: A Novel Aptamer Screening Process, Junkai Xie, Kalie Janece Dicks, Oscar C. Sanchez-Medina, Chongli Yuan
The Summer Undergraduate Research Fellowship (SURF) Symposium
Low-Cost diagnostic and screening tools are of vital importance for low resources countries like those in Africa. DNA aptamers are becoming an important detection analytical tool to recognize small molecule targets, drugs and metabolites. Compared to alternative recognition motifs, such as antibody, protein and peptides, aptamers are cheaper to produce via chemical synthesis, stable at room temperature and relatively faster in R&D lead time (year). Over the past 15 years, various aptamer based sensors have been developed. Conventionally, aptamers were screened via a Systematic Evolution of Ligands by EXponential enrichment(SELEX) process. We have improved the SELEX process to improve the …
Establishing A Lung Model For Evaluation Of Engineered Lung Microbiome Therapies, Kathryn F. Atherton, Stephen Miloro, Jenna Rickus
Establishing A Lung Model For Evaluation Of Engineered Lung Microbiome Therapies, Kathryn F. Atherton, Stephen Miloro, Jenna Rickus
The Summer Undergraduate Research Fellowship (SURF) Symposium
Benzene, a toxin and carcinogen found in air polluted by cigarette smoke, car exhaust, and industrial processes, is associated with the development of leukemia and lymphoma. Other than avoiding exposure, there is no current method to deter the effects of benzene. One potential strategy to prevent these effects is to engineer the bacteria of the human lung microbiome to degrade benzene. To evaluate this novel approach, we must verify that the bacteria remain viable within the lung microenvironment. To do so, lungs were harvested from rats and swabbed to determine the contents of the original lung microbiome. Then green fluorescent …
Gas-Based Perfusion Fmri Cerebrovascular Reactivity Maps And Time Of Arrival Maps, Jinxia Yao, Yunjie Tong, Matthew Robert Derdak
Gas-Based Perfusion Fmri Cerebrovascular Reactivity Maps And Time Of Arrival Maps, Jinxia Yao, Yunjie Tong, Matthew Robert Derdak
The Summer Undergraduate Research Fellowship (SURF) Symposium
Perfusion MRI is a promising tool used in assessing stroke, brain tumors, and patients with neurodegenerative diseases. However, common perfusion MRI techniques have several disadvantages, such as using exogenous contrast agents, low signal-to-noise ratio and long acquisition time. In this study, we used a computer-controlled gas delivery system RespirAct TM. This system provides a reliable carbon dioxide based vasoactive stimulus. This stimulus will immediately generate large and reliable functional magnetic resonance imaging (fMRI) signals, which can be used for perfusion imaging. Each subject was required to have three sequential magnetic resonance imaging (MRI) scans, which are structural scan, resting state …
The Effect Of An Enhanced Isopentenyl Monophosphate Pool On Terpenoid Biosynthesis In Vivo, Evan T. Adams, Laura K. Henry, Dr. Natalia Dudareva
The Effect Of An Enhanced Isopentenyl Monophosphate Pool On Terpenoid Biosynthesis In Vivo, Evan T. Adams, Laura K. Henry, Dr. Natalia Dudareva
The Summer Undergraduate Research Fellowship (SURF) Symposium
Found in all living organisms, terpenoids make up the largest group of natural products and are essential compounds for many major processes, including photosynthesis, respiration, hormone production, and electron transport. Additionally, they have commercial and medical value in products including fragrances, cosmetics, and medicines. Terpenoids originate from the five-carbon building blocks isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are synthesized by the mevalonic acid (MVA) and methylerithritol phosphate (MEP) pathways. An alternative MVA pathway was discovered in Archaea with the final two enzymes being phosphomevalonate decarboxylase (MPD) and isopentenyl phosphate kinase (IPK). Even though this alternative pathway is not …
Design And Development Of A Plasmid Vector For Protein Expression And Purification, Mahima Grover, Craig Sweet, David H. Thompson
Design And Development Of A Plasmid Vector For Protein Expression And Purification, Mahima Grover, Craig Sweet, David H. Thompson
The Summer Undergraduate Research Fellowship (SURF) Symposium
Production and isolation of proteins are difficult, costly and time-consuming processes. The aim of this project is for the development of plasmids, which allow for streamlined production and isolation of proteins. To allow for modular insertion of varying segments of DNA we are using ‘recursive directional ligation by plasmid reconstruction’. This technique uses type II restriction endonucleases, which cut downstream from their recognition site allowing multiple insertions without losing a restriction site. Using this process, we can ligate multiple DNA sequences together and express them to be able to construct a scar less fusion protein. In order to accomplish this, …
Characterizing The Rogfp2-Orp1 Fluorescent Biosensor For Detecting Oxidative Stress In Mammalian Cells, Sara A. Doan, Stevie Norcross, Mathew Tantama
Characterizing The Rogfp2-Orp1 Fluorescent Biosensor For Detecting Oxidative Stress In Mammalian Cells, Sara A. Doan, Stevie Norcross, Mathew Tantama
The Summer Undergraduate Research Fellowship (SURF) Symposium
Parkinson’s disease is a neurodegenerative disease involving the death of neurons in the substantia nigra and loss of the neurotransmitter, dopamine. The disease leads to progressive loss of motor control. Exact causes and mechanisms by which Parkinson’s disease proceeds are unknown, however, previous experiments determine oxidative stress in mitochondria as a factor that results in cell death. Strategies have been implemented to generate fluorescent biosensors to monitor reactive oxygen species (ROS) concentrations while simultaneously measuring the spatiotemporal distribution and correlation between the ROS, cellular function and organelle. Orp1, an enzyme found in yeast, is a sensitive oxidizing species and when …
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 …
Bio-Inspired Composite Hydrogels For Osteochondral Regenerative Engineering, Grant N. Gellert, Liangju Kuang, Chunhui Jiang, Nur P. Damayanti, Joseph Irudayaraj, Meng Deng
Bio-Inspired Composite Hydrogels For Osteochondral Regenerative Engineering, Grant N. Gellert, Liangju Kuang, Chunhui Jiang, Nur P. Damayanti, Joseph Irudayaraj, Meng Deng
The Summer Undergraduate Research Fellowship (SURF) Symposium
Treatment of osteochondral defects encompassing injury or degeneration to both the articular cartilage as well as the underlying subchondral bone presents a significant medical challenge. Current treatment options including autografts and allografts suffer from limited availability and risk of immunogenicity, respectively. The long term goal of this work is to develop an integrated scaffold system for treatment of osteochondral defects via in situ regeneration of bone, cartilage and the bone-cartilage interface. Hydrogels composed of polymer networks swollen in water provide an attractive biomaterial platform for regeneration of cartilage. In the present study, we have developed a novel composite hydrogel consisting …
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 …
The Effect Of Transient Hmg-Coa Reductase And 1-Deoxy-D-Xylulose-5-Phosphate Synthase Overexpression On Terpene Production In Transgenic Tomato Fruits, Scott A. Gentry, Michael Gutensohn, Laura Henry, Natalia Dudareva
The Effect Of Transient Hmg-Coa Reductase And 1-Deoxy-D-Xylulose-5-Phosphate Synthase Overexpression On Terpene Production In Transgenic Tomato Fruits, Scott A. Gentry, Michael Gutensohn, Laura Henry, Natalia Dudareva
The Summer Undergraduate Research Fellowship (SURF) Symposium
Isoprenoids are secondary metabolites that control numerous plant functions including signaling, growth, photosynthesis, and membrane structure. The bioengineering of isoprenoid synthesis could produce plants with a variety of beneficial traits. Plants form isoprenoids using two different pathways, the mevalonate (MVA) pathway and the methylerithritol phosphate (MEP) pathway, which cooperate via metabolic cross-talk. Transgenic tomato lines expressing both the plastidic and cytosolic forms of the snapdragon nerolidol/linalool terpene synthase under a fruit ripening specific promoter were transiently transformed to overexpress key enzymes in the two isoprenoid pathways. Hydroxymethylglutaryl-coenzyme A reductase (HMGR) is the rate limiting enzyme in the MVA pathway that …
Detection Of Foodborne Pathogens By Micro-Filtration Using A Continuous Cell Concentrator Device, Klaire E. Jeffries, Eduardo Ximenes, Michael R. Ladisch
Detection Of Foodborne Pathogens By Micro-Filtration Using A Continuous Cell Concentrator Device, Klaire E. Jeffries, Eduardo Ximenes, Michael R. Ladisch
The Summer Undergraduate Research Fellowship (SURF) Symposium
Protecting consumers from foodborne illness is an important health concern facing the food industry today. An important deficiency exposed by foodborne illness is the inability to track contaminated food back to the source in a timely manner. Although there are established methods that detect bacterial pathogen contamination, they are limited in distinguishing viable bacteria reliably and quickly. Currently, food pathogen testing requires lengthy culture steps, which many times are delayed even longer due to the lack of in-house testing labs. Typically, two to three days elapses between when the food is sampled and the test results are available. This study …
Bicistronic Design For Precise And Reliable Gene Expression, Nidhi N. Menon, Jenna Rickus
Bicistronic Design For Precise And Reliable Gene Expression, Nidhi N. Menon, Jenna Rickus
The Summer Undergraduate Research Fellowship (SURF) Symposium
Despite having progressed extensively in the field of synthetic biology in terms of DNA synthesis, analysis and transplanting, we still cannot reliably, quantitatively measure expression of new genetic constructs. We engineered a biobrick compatible expression cassette to control transcription and translation initiation which can be reused in new genetic contexts. Previous research has shown that the Bicistronic design have much lesser variations in expression with varying genes of interest as compared to the regular monocistronic design.(Mutalik, Endy, Guimaraes, Cambray, Lam, Juul, Tran & Paull, 2013) The Bicistronic design(BCD) consists of two Shine-Dalgarno sequences in its translation element which when combined …
Artificial Yeast Polarization Controlled By Chemical Gradient, James K. Nolan, Bernard Tao
Artificial Yeast Polarization Controlled By Chemical Gradient, James K. Nolan, Bernard Tao
The Summer Undergraduate Research Fellowship (SURF) Symposium
Engineering synthetic multicellular systems will lead to new synthetic biology technological platforms, inform developmental biology through recapitulation of natural systems and possibly unveil novel morphologies with practical applications not before reached throughout natural history (Maharbiz, 2012). Creating an exogenous molecular circuit that will polarize unicellular cells into “apical” and “basal” domains relative to a substrate plane would fulfill a missing component towards fully multicellular synthetic cellular communities (Maharbiz, 2012). To this end, a PIP3 polarization network previously designed by Chau and associates (Chau, Walter, Gerardin, Tang, Lim 2012) was coupled to the specific activation by niacin of a recombinant …
Development Of A Metabolomic Method To Define The Phenylalanome In Arabidopsis Thaliana, Cole G. Wunderlich, Clint Chapple, Xu Li
Development Of A Metabolomic Method To Define The Phenylalanome In Arabidopsis Thaliana, Cole G. Wunderlich, Clint Chapple, Xu Li
The Summer Undergraduate Research Fellowship (SURF) Symposium
In the study of metabolomics, one of the greatest challenges can be accurately identifying compounds detected in biological extracts, especially when standards are not readily available. Current metabolomic methods are also limited in that they provide little to no information about a compound’s metabolic origin. In this study, we sought to address these issues by developing a novel metabolomic method that employs stable isotope feeding, LC-MS, Xcms, and an analytical software algorithm to study the ‘phenylalanome’ of Arabidopsis thaliana. Using this approach we were able to develop a method that, based on current results, is capable of detecting over …
Fabrication Of Multilayered Structure For Coherent Random Lasing, John Rauchenstein, Young L. Kim
Fabrication Of Multilayered Structure For Coherent Random Lasing, John Rauchenstein, Young L. Kim
The Summer Undergraduate Research Fellowship (SURF) Symposium
High powered lasers have many applications, including medical treatment and surgery. However, these lasers are extremely expensive and are therefore not widely available. The aim of this study was to demonstrate a method to create such a laser with significantly decreased overall cost and increased efficiency. In order to do this, we explored a phenomenon called random lasing which is a light amplification process. To start with, a low-cost pumping laser is directed at normal incidence toward a multi-layered sample with two alternating layers. At first pearl, a naturally found material that has many organic nano-scale layers (similar to the …