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- Drosophila (2)
- Fluorescence Resonance Energy Transfer (2)
- Larrea Tridentata (2)
- Molecular dynamics (2)
- Tissue Engineering (2)
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- Two-Photon Microscopy (2)
- Antibiotic resistance (1)
- Antibiotics (1)
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- Biophotonics (1)
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- CARBON QUANTUM DOTS (1)
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- COVID-19 (1)
- Cafeteria roenbergensis (1)
- Capsid (1)
- Capsid assembly (1)
- Chagas Disease (1)
- Ciberinfrastructure (1)
- Circadian rhythm (1)
- Circular dichroism (1)
- Computational biology (1)
- Confocal Raman microscopy (1)
- Conservation (1)
- Cruzain (1)
- Cryo-EM (1)
- Cyclic Adenosine Monophosphate (1)
- DNA repair (1)
- DRUG DELIVERY (1)
- DelPhi (1)
Articles 1 - 29 of 29
Full-Text Articles in Physical Sciences and Mathematics
Assessing Nordihydroguaiaretic Acid Properties And Its Potential Therapeutic Effect For Glioblastoma, Jose Arturo Guerrero
Assessing Nordihydroguaiaretic Acid Properties And Its Potential Therapeutic Effect For Glioblastoma, Jose Arturo Guerrero
Open Access Theses & Dissertations
This study employs a combination of theoretical and experimental analysis to spectroscopically investigate the biomechanistic structure relationship and therapeutic effects of the Nordihydroguaiaretic Acid (NDGA) chemical derived from the Larrea Tridentata plant. These relationships are crucial for understanding NDGA's efficacy in disease prevention, treatment, and potential toxicological effects. While the medicinal and antiviral properties of the NDGA have been studied extensively, there remains a gap in optically identifying and reporting its structural changes. The current research successfully reveals evident trends in NDGA's vibrational signatures, particularly highlighting the absence of the Raman feature at 780 〖cm〗^(-1) as indicative of a fully …
Analysis Of The Electrostatic Characteristics Of The Zika Virus Capsid Using Computational Methods, Cassandra Guadalupe Del Rio De Avila
Analysis Of The Electrostatic Characteristics Of The Zika Virus Capsid Using Computational Methods, Cassandra Guadalupe Del Rio De Avila
Open Access Theses & Dissertations
Zika virus (ZIKV) is a flavivirus that is usually transmitted through the bite of infected mosquitoes. This virus can cause a variety of neurological disorders, the most common being Guillain-Barré syndrome in adults. Moreover, it is of great concern in pregnant women, since can cause deformities in the brain and other organs of newborns.Studying the structural characteristics of the virus during its mature and infectious phase can provide crucial information on the mechanisms by which it enters and replicates within host cells, as well as its evolution, transmission, and interaction with other living organisms. The symmetric pattern present in the …
Microscopic And Spectroscopic Analysis Of Nordihydroguaiaretic Acid Effect On Astrocytes, Lizbeth Vanessa Martinez Lopez
Microscopic And Spectroscopic Analysis Of Nordihydroguaiaretic Acid Effect On Astrocytes, Lizbeth Vanessa Martinez Lopez
Open Access Theses & Dissertations
Astrocytes, one of the most abundant cell components in the central nervous system (CNS), have been a research target in the last few years. Several studies have found that astrocytes are not only mere supporters of neurons but also of essential processes developed in the CNS. Their malfunction could induce neurodegenerative diseases and brain tumors. Thus, further understanding of astrocytes and their role is of high interest to develop possible new treatments and methods of disease diagnosis, especially in brain cancer. The plant Larrea tridentata (La Gobernadora in Mexico or Creosote bush in the United States) is known to have …
Developing And Applying Computational Methods On Biomolecules, Shengjie Sun
Developing And Applying Computational Methods On Biomolecules, Shengjie Sun
Open Access Theses & Dissertations
Computational biophysics is an interdisciplinary subject that uses numerical algorithms to study the physical principles underlying biological phenomena and processes. Electrostatic interactions play an important role in computational molecular biophysics and their potential impact on disease mechanisms. At distances larger than several Angstroms, electrostatic interactions dominate all other forces, while the alteration of short-range electrostatic pairwise interactions can also have significant effects. The dual nature of electrostatic interactions, being dominant at long-range and specific at short-range, underscores their profound implications for wild-type structure and function. Any disruption of the complex electrostatic network of interactions may abolish wild-type functionality and could …
Lipid Rafts, Exosomal Vesicles And Anti-Giardial Therapies, Brian Ivan Grajeda
Lipid Rafts, Exosomal Vesicles And Anti-Giardial Therapies, Brian Ivan Grajeda
Open Access Theses & Dissertations
Giardia lamblia, a protozoan parasite, is a major cause of waterborne infection, worldwide. While the trophozoite form of this parasite induces pathological symptoms in the gut, the cyst forms transmit the infection via contaminated water. Since Giardia is a non-invasive parasite, the actual mechanism by which it causes infection remains elusive. We have previously reported that Giardia assembles cholesterol and GM1 glycolipid-enriched lipid rafts (LRs) that participate in encystation and cyst production. To further delineate the role of LRs in pathogenesis, we isolated LRs from Giardia and subjected them to proteomic analysis. Various cellular proteins including the virulent proteinsâe.g., giardins, …
Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie
Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie
Open Access Theses & Dissertations
Computational biology is an interdisciplinary area that applies computational approaches in biological big data, including protein amino acid sequences, genetic sequences, etc., which is widely used to analyze protein-protein interactions, make predictions in drug discovery, develop vaccines, etc. Popular methods include mathematical modeling, molecular dynamics simulations, data science mythology, etc. With the help of computational algorithms and applications, drug development is much faster than traditional processes, as it reduces risks early on in a drug discovery process and helps researchers select target candidates that have the highest potential for success. In my doctoral research, I applied multi-scale computational approaches to …
Nanotechnology-Based Approaches To Mitigate Environmental Pollutants -- Induced Neurological Disorders, Jyoti Ahlawat
Nanotechnology-Based Approaches To Mitigate Environmental Pollutants -- Induced Neurological Disorders, Jyoti Ahlawat
Open Access Theses & Dissertations
Neurodegenerative diseases such as Parkinson's disease (PD), Alzheimerâ??s Disease (AD) and Huntingtonâ??s Disease (HD) have no cure despite intensive research efforts geared towards therapeutics development. In the USA, patients with PD and AD alone cost the nation ~ $200 billion annually in patient care and lost productivity. Therefore, there remains an urgent and unmet need to develop novel drugs and drug carriers with the potential to slow down, halt and ideally reverse the course of neurodegenerative disorders. The dissertation focuses on developing approaches towards targeting PD using multifactorial mechanisms including the targeting of protein aggregation and oxidative stress. This is …
Pacific Black Duck Ecology And Habitat Assessment In Aunu'u, American Samoa, And Their Relationship To Other Mallard-Like Ducks Of Oceania, Greater Indonesia, And The Philippines, Marissa Kaminski
Open Access Theses & Dissertations
Determining a species’ ecological needs, assessing the quality of their habitat, and determining genetic differentiation and connectivity among populations is essential to their conservation. My dissertation focuses on obtaining such a holistic view for a population of Pacific Black Ducks recently established on the Island of Aunu’u, American Samoa. Specifically, I present the first evaluation of the ecology and habitat of a recently established population of Pacific Black Ducks on the Island of Aunu’u, American Samoa, in Chapter 1, while I assess the genetic connectivity and relationship of this population to other Mallard-like ducks found in Greater Indonesia, Oceania, and …
The Hybridizing Ions Treatment (Hit) Method Development And Computational Study On Sars-Cov-2 E Protein., Shengjie Sun
The Hybridizing Ions Treatment (Hit) Method Development And Computational Study On Sars-Cov-2 E Protein., Shengjie Sun
Open Access Theses & Dissertations
Fast and accurate calculations of the electrostatic features for highly charged biomolecules such as DNA, RNA, highly charged proteins, are crucial but challenging tasks. Traditional implicit solvent methods calculate the electrostatic features fast, but they are not able to balance the high net charges in the biomolecules effectively. Explicit solvent methods add unbalanced ions to neutralize the highly charged biomolecules in molecular dynamic simulations, which require more expensive computing resources. Here we developed a novel method, the Hybridizing Ions Treatment (HIT) method, which hybridizes the implicit solvent method with the explicit method to realistically calculate the electrostatic potential for highly …
Structural Characterization Of Two Large Icosahedral Dna Viruses And Their Capsid Assembly Mechanisms, Yuejiao Xian
Structural Characterization Of Two Large Icosahedral Dna Viruses And Their Capsid Assembly Mechanisms, Yuejiao Xian
Open Access Theses & Dissertations
In the last three decades, many large DNA viruses were discovered and grouped into a loosely defined clade of Nucleocytoplasmic Large DNA Viruses (NCLDVs). NCLDVs infect a wide range of hosts from single cellular protists to large animals. Recently, these viruses were classified as a new phylum of Nucleocytoviricota under the kingdom of Bamfordvirae. The genomes of these Nucleocytoviricota viruses (NCVs) are remarkedly large and complicated, containing many cellular genes from all three domains of life, which raised intensive debates on their evolutionary origins. Despite being classified in the same phylum, their physical structures vary and can be roughly classified …
Antioxidant Intervention In Radical-Induced Protein Damage, Emmanuel Zubia
Antioxidant Intervention In Radical-Induced Protein Damage, Emmanuel Zubia
Open Access Theses & Dissertations
Many environmental toxicants are known to increase free-radical production, which can create cellular havoc and lead to a myriad of ailments. Antioxidants can be used to ameliorate the prevalence of free radicals, potentially serving as prophylactics against radical-induced disorders. Many exogenous antioxidants are phytochemicals in origin, such as ascorbic acid, gallic acid, and ellagic acid. Some of these antioxidants can be found in traditional medicine, like tanshinone and brazilin, which have been studied and are known to have low cytotoxicity. Here we test the radical rescue capacity of a selected group of phytochemical antioxidants on protein rescue models. Specifically, our …
Expression, Purification, And Characterization Of Recombinant Human Npas2, Brenda Moreno
Expression, Purification, And Characterization Of Recombinant Human Npas2, Brenda Moreno
Open Access Theses & Dissertations
Many living organisms have biological clocks known as circadian rhythms that control various physiological and behavioral processes, tailored with the day and night. At the cellular level, the circadian clock drives daily rhythms with a transcriptional-translational feedback loop (TTFL) established by multiple transcription factors and genes under their regulation. Circadian Locomotor Output Cycles Kaput (CLOCK) and Brain and Muscle ARNT-like protein 1 (BMAL1) are two of those transcription factors, initiating the TTFL by forming a heterodimeric complex that bind to DNA promoters. Neuronal PAS domain protein 2 (NPAS2) is a functional analog to CLOCK. Less knowledge about NPAS2, in contrast …
Non Linear Optics For Materials Fabrication And Medical Instrumentation, Aurelio Paez
Non Linear Optics For Materials Fabrication And Medical Instrumentation, Aurelio Paez
Open Access Theses & Dissertations
Two-photon absorption is a nonlinear optical process where two photons are absorbed by a molecule simultaneously. The probability of this quantum phenomenon is proportional to the quadratic excitation of light intensity. It has many applications in biomedical and materials research, such as two-photon fluorescence microcopy. The first project is to apply two-photon absorption induced bond cleavage in photoreactive materials for engineering 3D tissue scaffolds. The major challenge for growing thick 3D tissues is the lack of vasculature, where nutrients and oxygen can be delivered to the growing cells. Our collaborators have synthesized a novel polypeptide that is composed of 34-mer …
Potential Of Nanoscale Elements To Control Fusarium Wilt Disease In Tomato (Solanum Lycopersicum), Enhance Macronutrient Use Efficiency, And Increase Its Yield, Ishaq Olarewaju Adisa
Potential Of Nanoscale Elements To Control Fusarium Wilt Disease In Tomato (Solanum Lycopersicum), Enhance Macronutrient Use Efficiency, And Increase Its Yield, Ishaq Olarewaju Adisa
Open Access Theses & Dissertations
Nanotechnology has a great potential in ensuring food production, security and safety globally. Over the past decade, research on the use of nanomaterials to supply nutrient elements and protect plants from pest and diseases has significantly increased. Tomato (Solanum lycopersicum) is one of the most consumed vegetables in the world and United State is one of its largest producers globally generating billions of dollars annually in revenue.. Tomato plants are affected worldwide by Fusarium wilt caused by Fusarium oxysporum f. sp. Lycopersici. There is growing concern about excessive use of conventional pesticides in controlling Fusarium and other diseases in tomato …
Geant4 Study Of A Gamma Ray Collimator For Proton Therapy, Selim Romero
Geant4 Study Of A Gamma Ray Collimator For Proton Therapy, Selim Romero
Open Access Theses & Dissertations
This Thesis presents the results of an investigation of the use of collimators in proton therapy. The problem to solve is that in the proton therapy, we do not have the certainty if the target-tumor is receiving all the energy to destroy it or if we are really shooting at this one, so the remaining question is: where the beam is hitting? How to know it? to answer those questions our work has the propose of study proton therapy to determine where the proton interactions occur, these kinds of interactions usually produce gamma rays, and we simulated in GEANT4 the …
Environmental And Genetic Factors Affecting Antibiotic Resistance Of Extended Spectrum Î?-Lactamase Bacteria From The Rio Grande River In El Paso, Tx And Cd. Juarez, Mexico, Maria D. Fuentes
Open Access Theses & Dissertations
Background: The Rio Grande River provides a major source of potable and agricultural water for the population of the Texas/Mexico border region. Cattle farming and ranching are the most prevalent activities, which may contribute to the microbial burden of pharmaceuticals into our state's water resources. Antibiotics, presumably released into the environment by discharges originating from waste-water treatment plants, septic disposal systems, animal feeding operations and urban runoff have a definite impact on the ecosystem and may contribute to an increase in antibiotic resistance. We hypothesized that waters of the Rio Grande River contained Multi Drug Resistant Organisms (MDRO) and mobile …
The Inverse And Direct Hofmeister Series Of Hen Egg White Lysozyme At Ph Below The Isoelectric Point (Pi) As Seen By Small Angle X-Ray Scattering(Saxs), Pawan Koirala
Open Access Theses & Dissertations
The structural changes of Hen Egg White Lysozyme (HEWL) in the intermediate stages leading up to Hofmeister anion-induced aggregation were measured using small-angle x-ray Scattering (SAXS). We used three concentrations of HEWL: 10mg/ml, 60mg/ml and 200mg/ml and two concentrations of salts: 0.1M and 1.0M, mostly in a Tris-buffer solution with a pH of 9.0. For 200mg/ml in Di-water solution, the scattering signal was best fit using an ellipsoidal form factor with equatorial radius of 28.4±0.1 Å and polar radius of 11.3±0.1 Å, and a screened Coulomb repulsive structure factor with an effective radius of 19.9±0.1 Å and protein surface charge …
Integrated Immunoassays On Paper/Polymer Hybrid Microfluidic Devices For Low-Cost Detection Of Disease Biomarkers, Sanjay Sharma Timilsina
Integrated Immunoassays On Paper/Polymer Hybrid Microfluidic Devices For Low-Cost Detection Of Disease Biomarkers, Sanjay Sharma Timilsina
Open Access Theses & Dissertations
Infectious diseases and cancers have been the major cause of global death and disability causing a significant impact on global health and economies. Enzyme-linked immunosorbent assay (ELISA) is one of the most widely used laboratory diagnostic methods for infectious diseases and cancer. ELISA detects proteins based on their binding to immobilized antibodies or antigen. Even though most ELISAs performed today in 96-well plates are well suited for high throughput assays, performing ELISA in low-resource settings is limited by several factors, such as long incubation time, large volumes of precious reagents, and well-equipped laboratories. Herein, we have developed multiple simple, miniaturized …
Imaging Live Drosophila Brain With Two-Photon Fluorescence Microscopy, Syeed Ehsan Ahmed
Imaging Live Drosophila Brain With Two-Photon Fluorescence Microscopy, Syeed Ehsan Ahmed
Open Access Theses & Dissertations
Two-photon fluorescence microscopy is an imaging technique which delivers distinct benefits for in vivo cellular and molecular imaging. Cyclic adenosine monophosphate (cAMP), a second messenger molecule, is responsible for triggering many physiological changes in neural system. However, the mechanism by which this molecule regulates responses in neuron cells is not yet clearly understood. When cAMP binds to a target protein, it changes the structure of that protein. Therefore, studying this molecular structure change with fluorescence resonance energy transfer (FRET) imaging can shed light on the cAMP functioning mechanism. FRET is a non-radiative dipole-dipole coupling which is sensitive to small distance …
Two-Photon Excitation Based Photochemistry And Neural Imaging, Kevin Andrew Hatch
Two-Photon Excitation Based Photochemistry And Neural Imaging, Kevin Andrew Hatch
Open Access Theses & Dissertations
Two-photon microscopy is a fluorescence imaging technique which provides distinct advantages in three-dimensional cellular and molecular imaging. The benefits of this technology may extend beyond imaging capabilities through exploitation of the quantum processes responsible for fluorescent events. This study utilized a two-photon microscope to investigate a synthetic photoreactive collagen peptidomimetic, which may serve as a potential material for tissue engineering using the techniques of two-photon photolysis and two-photon polymerization. The combination of these techniques could potentially be used to produce a scaffold for the vascularization of engineered three-dimensional tissues in vitro to address the current limitations of tissue engineering. Additionally, …
Study On Dioxygen Binding To Heme Using Scan Functional, Zegnet Yimer Muhammed
Study On Dioxygen Binding To Heme Using Scan Functional, Zegnet Yimer Muhammed
Open Access Theses & Dissertations
Density functional theory, a quantum mechanical based electronic structure method with GGA-PBE and MGG-SCAN functionals, are used to investigate the structure and energies of singlet, triplet, and quintet spin states of FeP (iron Porphyrin), FePIm (imidazole iron porphyrin), and FePImO2 (dioxygen imidazole iron porphyrin) systems. The binding and release of dioxygen to and from hemoglobin (Hb) are the most crucial reaction takes place in human body to sustain the existence of life. FePImO2 is used to model this phenomenon. When O2 binds to FePIm, the system undergoes a conformational change. i.e. from domed structure of FePIm in which the Fe …
The Characterization Of A Recombinant Virophage Integrase, Martin Christopher Chacon
The Characterization Of A Recombinant Virophage Integrase, Martin Christopher Chacon
Open Access Theses & Dissertations
Virophages are satellite-like dsDNA viruses that parasitize giant viruses of the family Mimiviridae. Mavirus is the second virophage discovered that associates with its host virus Cafeteria roenbergensis Virus (CroV). When co-infecting their common host cell Cafeteria roenbergensis, a marine zooplankton that is widely spread throughout the oceans, mavirus will inhibit CroV's replication. In addition, mavirus was shown to share high similarities to the Maverick/Polinton eukaryotic DNA transposons. A coding sequence in mavirus genome (MV02) reveals high homology to retroviral integrases such as those found in HIVs. The putative integrase MV02 is predicted to integrate mavirus DNA into the host genome. …
Identifying Non-Classical Active Sites As A Tool For Enzyme Inhibition, Marisol Serrano
Identifying Non-Classical Active Sites As A Tool For Enzyme Inhibition, Marisol Serrano
Open Access Theses & Dissertations
Chagas disease, caused by the parasite Trypanosoma cruzi, is an endemic life-threatening disease that affects mainly the heart. It remains the leading cause of heart failure in Latin American countries. Since current treatments against this parasite are highly toxic and somewhat ineffective, novel and more efficacious types of interventions are desired. Cruzain, identified as the major cathepsin for T. cruzi, plays a major role in the parasite's life cycle; making this enzyme very attractive for potential trypanocidal drugs discovery. The recombinant cruzain is synthesized as a zymogenic pro-protein (PCZN) which possesses a pro domain and a catalytic domain. In this …
Studying Cellular And Molecular Interaction With Two-Photon Fluorescence Microscopy, Arifur Rahaman
Studying Cellular And Molecular Interaction With Two-Photon Fluorescence Microscopy, Arifur Rahaman
Open Access Theses & Dissertations
Advances in microscopy and fluorescent probes provide new insight into studying cellular and molecular interactions. Two-photon fluorescence microscopy is one of the most important recent inventions in cellular and molecular study. This technology enables noninvasive study at cellular and molecular levels in three dimensions with submicrometer resolution. Two-photon excitation of fluorophores results from the simultaneous absorption of two photons. This excitation process has a number of unique advantages, such as reduced specimen photodamage and enhanced penetration depth. In this study, we used our two-photon microscope to observe predatorial behavior of fast moving bacterivorous marine organism Cafeteria roenbergensis and quantify Mycobacterium …
Evaluation Of Small Molecules On The Excitatory Amino Acid Transporter 3 (Eaat3) For The Treatment Of Ocd, Emmanuel Zubia
Evaluation Of Small Molecules On The Excitatory Amino Acid Transporter 3 (Eaat3) For The Treatment Of Ocd, Emmanuel Zubia
Open Access Theses & Dissertations
We seek to discover new drug candidates for the excitatory amino acid transporter 3 (EAAT3) for the treatment of Obsessive Compulsive Disorder (OCD). We hypothesize that decreasing the glutamatergic transmission via EAAT3 intervention will create an amelioration of the symptoms of OCD. For this we have prepared in-silico binding calculations to identify a better compound that can stimulate EAAT3 and decrease glutamatergic transmission. This research will help us further understand and elucidate the role of glutamate in the neural mechanisms of this illness, which to date remain inconclusive. Those areas of study are significant because, until now, there is no …
Role Of Small Molecules In Rescuing Protein Folding Under Oxidative Stress, Mahmoud Fawzi Megahed Helal Khalil
Role Of Small Molecules In Rescuing Protein Folding Under Oxidative Stress, Mahmoud Fawzi Megahed Helal Khalil
Open Access Theses & Dissertations
Increased levels of nitrosative stress intracellularly within the endoplasmic reticulum is a key factor involvled in the pathogenesis of both Parkinson's (PD) and Alzheimer's (AD) diseases. Previous in-vitro studies in our lab showed that increased levels of nitrosative stress lead to aggregation of misfolded proteins and formation of Lewy Bodies, the main biomarker of PD and AD diseases. Although this was mainly through nitrosylation of Protein Disulfide Isomerase (PDI), the chief endoplasmic reticulum (ER) resident oxidoreductase chaperone responsible for maturation of disulfide-bond-containing proteins, we demonstrate in this project that increased levels of nitrosative stress has an additional direct effect on …
Biochemical Characterization Of Four Distinct Proteins, Gustavo A. Avila
Biochemical Characterization Of Four Distinct Proteins, Gustavo A. Avila
Open Access Theses & Dissertations
Proteins are ubiquitous in all living organisms, executing the majority of cellular functions in distinct ways. Understanding a protein's role necessitates investigating its structure and function, which are closely related. My research couples these two aspects by delving into the biochemical and structural characterization of proteins in four distinct systems, all playing central roles in numerous significant disease progressions. These four original research endeavors were all targeted for structural studies with a unifying relationship to establish our new structural biochemistry lab. These four systems are: (1) Gam1, an early adenovirus protein globally inhibiting host SUMOylation; (2) Anthrax toxin complexed with …
Furthering Our Understanding And Assessing The Effectiveness Of Scaling Patterns And Controls Of Land-Atmosphere Carbon Exchange In A Shrubland Of The Chihuahuan Desert With Novel Cyberinfrastructure, Aline Jaimes
Open Access Theses & Dissertations
Over the last century, arid and semiarid regions have undergone intense desertification and in many regions, vegetation has shifted from grassland to shrubland dominated ecosystems. This land cover change has important implications for how desert ecosystems function - especially with regards to land-atmosphere exchange of carbon, water, and energy. Although the extent of desertified landscapes is expected to expand over the next 30 to 40 years, there is a relatively poor understanding of how this state transition will impact ecosystem function and feedbacks to other components of the earth system. Key to addressing this challenge is an improved understanding of …
Refining Molecular Approaches For Bacterial Source Tracking (Bst) In Texas, Joy Truesdale
Refining Molecular Approaches For Bacterial Source Tracking (Bst) In Texas, Joy Truesdale
Open Access Theses & Dissertations
Bacterial source tracking (BST) is a new science that aids in identifying sources of human and animal fecal contamination of environmental water. There are currently two approaches used in BST, library-dependent and library-independent methods. The fecal bacterium E. coli is often used in library dependent methods because it indicates fecal contamination, has been used in human health risk assessments, and has water quality regulatory significance. A disadvantage of E. coli library dependent BST methods is that identification libraries of E. coli isolated from known fecal sources are needed to identify the sources of E. coli isolated from water samples. Further, …