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Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan 2019 Collin College

Assessing The Potential Impact Of Nanotechnology On The Purification Of Water, Noor Khan

Quest

Independent Research Paper

Research in progress for PHYS 2426: University Physics II

Faculty Mentor: Raji Kannampuzha, Ph.D.

The following paper represents research work done by students in a University Physics 2426 class, the second half of a two-semester introductory course in physics. It is a calculus-based physics course, intended primarily for physics, chemistry, math, and engineering majors. Students are introduced to the concept of academic research by learning to ask research-focused questions and then use the library resources to pursue outside research to find answers. For this assignment, students are asked to investigate a physical science, biological science, or ...


Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau 2019 Iowa State University

Two Distinct Domains Contribute To The Substrate Acyl Chain Length Selectivity Of Plant Acyl-Acp Thioesterase, Fuyuan Jing, Le Zhao, Marna D. Yandeau-Nelson, Basil J. Nikolau

Basil Nikolau

The substrate specificity of acyl-ACP thioesterase (TE) plays an essential role in controlling the fatty acid profile produced by type II fatty acid synthases. Here we identify two groups of residues that synergistically determine different substrate specificities of two acyl-ACP TEs from Cuphea viscosissima (CvFatB1 and CvFatB2). One group (V194, V217, N223, R226, R227, and I268 in CvFatB2) is critical in determining the structure and depth of a hydrophobic cavity in the N-terminal hotdog domain that binds the substrate’s acyl moiety. The other group (255-RKLSKI-260 and 285-RKLPKL-289 in CvFatB2) defines positively charged surface patches that may facilitate binding of ...


Elucidating The Mechanism Of Action Of Experimental Compound Sw33 In Toxoplasma Gondii, Sean Watson 2019 University of Nebraska at Omaha

Elucidating The Mechanism Of Action Of Experimental Compound Sw33 In Toxoplasma Gondii, Sean Watson

Theses/Capstones/Creative Projects

In recent years, antimicrobial drug resistance has become widespread and thus triggered an ever-growing need for the development of new, efficacious drug treatments. As an antimicrobial drug is developed, its mechanism of action is often identified before it becomes a potential candidate for clinical use. One potential method for identifying mechanism of action is chemical mutagenesis, in which induction of drug-resistant populations is followed by whole-genome sequencing of several clonal isolates. The subsequent observation of identical point mutations in the same gene across multiple drug-resistant populations can indicate a likely molecular target. However, this technique lacks the capacity to facilitate ...


Design And Application Of Matrix Metalloproteinase-9-Responsive Peptide Nanostructures, Jiye Son 2019 The Graduate Center, City University of New York

Design And Application Of Matrix Metalloproteinase-9-Responsive Peptide Nanostructures, Jiye Son

All Dissertations, Theses, and Capstone Projects

Matrix metalloproteinase (MMP)-responsive materials have been investigated since the late 1990’s as scaffolds for tissue engineering and since then, have evolved into sophisticated nanomaterials for cancer-targeting therapy. In this thesis titled, “Design and Application of Matrix Metalloproteinase-9-Responsive Peptide Nanostructures,” we aim to answer the following key questions: can MMP-responsive nanomaterials improve the efficacy of anti-cancer treatments? How can we achieve specificity towards MMPs using nanomaterials? Finally, what are the advantages in using peptides as building blocks to create MMP-responsive nanostructures? Each chapter in the thesis will address one or more of the key questions and draw conclusions at ...


Biotechnology And Pest Resistance: An Economic Assessment Of Refuges, Terrance M. Hurley, Bruce A. Babcock, Richard L. Hellmich 2019 Iowa State University

Biotechnology And Pest Resistance: An Economic Assessment Of Refuges, Terrance M. Hurley, Bruce A. Babcock, Richard L. Hellmich

Richard L Hellmich

Biologists now engineer transgenic crop varieties that offer farmers a new tool for effectively managing pests. Concern over pest resistance, however, has prompted the Environmental Protection Agency to require resistance management plans. This paper develops an economic model of pest management with pest resistance to estimate the constant proportion of cropland planted in refuge that maximizes farm income over a fixed planning horizon. Results indicate a clear economic tradeoff between the pest control benefits of a transgenic variety and the resistance management benefits afforded by refuge.


Uptake And Persistence Of Bacterial Magnetite Magnetosomes In A Mammalian Cell Line: Implications For Medical And Biotechnological Applications., Jefferson Cypriano, Jacques Werckmann, Gabriele Vargas, Adrana Lopes dos Santos, Karen T. Silva, Pedro Leao, Fernando P. Almeida, Dennis A. Bazylinski, Marcos Farina, Ulysses Lins, Fernanda Abreu 2019 Universidade Federal do Rio de Janeiro

Uptake And Persistence Of Bacterial Magnetite Magnetosomes In A Mammalian Cell Line: Implications For Medical And Biotechnological Applications., Jefferson Cypriano, Jacques Werckmann, Gabriele Vargas, Adrana Lopes Dos Santos, Karen T. Silva, Pedro Leao, Fernando P. Almeida, Dennis A. Bazylinski, Marcos Farina, Ulysses Lins, Fernanda Abreu

Life Sciences Faculty Publications

Magnetotactic bacteria biomineralize intracellular magnetic nanocrystals surrounded by a lipid bilayer called magnetosomes. Due to their unique characteristics, magnetite magnetosomes are promising tools in Biomedicine. However, the uptake, persistence, and accumulation of magnetosomes within mammalian cells have not been well studied. Here, the endocytic pathway of magnetite magnetosomes and their effects on human cervix epithelial (HeLa) cells were studied by electron microscopy and high spatial resolution nano-analysis techniques. Transmission electron microscopy of HeLa cells after incubation with purified magnetosomes showed the presence of magnetic nanoparticles inside or outside endosomes within the cell, which suggests different modes of internalization, and that ...


The Pharmabiotic For Phenylketonuria: Development Of A Novel Therapeutic, Chloé Elizabeth LeBegue 2019 University of South Carolina

The Pharmabiotic For Phenylketonuria: Development Of A Novel Therapeutic, Chloé Elizabeth Lebegue

Senior Theses

Phenylketonuria, now known as phenylalanine hydroxylase (PAH) deficiency, is a genetic disorder of metabolism affecting approximately one in every 15,000 infants born in the United States. Patients have nonfunctional PAH enzyme secondary to one or more genetic mutations. The enzyme deficit results in destructive supraphysiologic blood phenylalanine levels upon consumption of the essential dietary amino acid phenylalanine. Current standards of care mitigate signs and symptoms of the disorder, but do not approach a cure. The methods for creating a prototype pharmabiotic as an innovative treatment strategy for PAH deficiency are described herein.

DNA molecular cloning techniques were utilized to ...


Space Race, Siri And The Central Dogma: A Contemporary Nursing Analysis Of Antibiotics Resistance, Donovan Lucibello 2019 Carroll College

Space Race, Siri And The Central Dogma: A Contemporary Nursing Analysis Of Antibiotics Resistance, Donovan Lucibello

Nursing Undergraduate Theses

In the age of information, antibiotic resistance is still a black-box problem in clinical practice; pathogens are often defined in terms of which pharmaceuticals are no longer effective, and treatment protocols are prescribed prophylactically; often at strengths that are in excess of what is known about the pathogen’s susceptibilities or even its identity. All antibiotic resistance mechanisms involve the expression of proteins that provide resistance capabilities. These modified proteins should be detectable by analyzing DNA (or RNA intermediates) that code for them in order to determine a pathogen’s threat profile. Next-Generation and nanopore DNA sequencing technologies are capable ...


Visual Contributions To Balance Control During Gait, Kyle Brozek 2019 University of Nebraska at Omaha

Visual Contributions To Balance Control During Gait, Kyle Brozek

Student Research and Creative Activity Fair

We propose to isolate the contributions of continuous OF to the orthogonal relationship between balance and gait control during treadmill walking using a series of conditions. Manipulating the direction of OF using a CAREN (Motek Medical, Amsterdam, Netherlands) virtual reality treadmill environment will isolate these visual contributions in human subjects as they walk. We plan to tease out the effect of OF direction on the relationship between gait and balance control by having healthy young adults perform a series of treadmill walking trials while immersed in a VR environment. This will be done by manipulating the direction of walking and ...


Day To Day And Leg To Leg Variation In Gene Expression, Zohal Alizai 2019 University of Nebraska at Omaha

Day To Day And Leg To Leg Variation In Gene Expression, Zohal Alizai

Student Research and Creative Activity Fair

BACKGROUND: Skeletal muscle biopsies are extensively used in research to determine the effects of exercise. Usually, sequential biopsies are taken before and after exercise in order to determine the influence of exercise on gene expression. Often it is not clear if the results are due to exercise or as a result of damage cause by the biopsy to the muscle. Previous studies have proven that multiple biopsies in the same leg cause stress to the muscle and such stress leads to inflammation and other response pathways that alter the gene expression. PURPOSE: The purpose of this study is to determine ...


Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao 2019 Southern Methodist University

Allosteric Mechanism Of The Circadian Protein Vivid Resolved Through Markov State Model And Machine Learning Analysis, Hongyu Zhou, Zheng Dong, Gennady M. Verkhivker, Brian D. Zoltowski, Peng Tao

Mathematics, Physics, and Computer Science Faculty Articles and Research

The fungal circadian clock photoreceptor Vivid (VVD) contains a photosensitive allosteric light, oxygen, voltage (LOV) domain that undergoes a large N-terminal conformational change. The mechanism by which a blue-light driven covalent bond formation leads to a global conformational change remains unclear, which hinders the further development of VVD as an optogenetic tool. We answered this question through a novel computational platform integrating Markov state models, machine learning methods, and newly developed community analysis algorithms. Applying this new integrative approach, we provided a quantitative evaluation of the contribution from the covalent bond to the protein global conformational change, and proposed an ...


Heterodera Glycines Utilizes Promiscuous Spliced Leaders And Demonstrates A Unique Preference For A Species-Specifc Spliced Leader Over C. Elegans Sl1, Stacey N. Barnes, Rick E. Masonbrink, Tom R. Maier, Arun S. Seetharam, Anoop S. Sindhu, Andrew J. Severin, Thomas J. Baum 2019 Iowa State University

Heterodera Glycines Utilizes Promiscuous Spliced Leaders And Demonstrates A Unique Preference For A Species-Specifc Spliced Leader Over C. Elegans Sl1, Stacey N. Barnes, Rick E. Masonbrink, Tom R. Maier, Arun S. Seetharam, Anoop S. Sindhu, Andrew J. Severin, Thomas J. Baum

Office of Biotechnology Publications

Spliced leader trans-splicing (SLTS) plays a part in the maturation of pre-mRNAs in select species across multiple phyla but is particularly prevalent in Nematoda. The role of spliced leaders (SL) within the cell is unclear and an accurate assessment of SL occurrence within an organism is possible only after extensive sequencing data are available, which is not currently the case for many nematode species. SL discovery is further complicated by an absence of SL sequences from high-throughput sequencing results due to incomplete sequencing of the 5'-ends of transcripts during RNA-seq library preparation, known as 5'-bias. Existing datasets and ...


Identification And Characterization Of Barrier Insulator Activity In The T-Cell Receptor Alpha Locus Control Region, Gayathri Devi Raghupathy 2019 The Graduate Center, City University of New York

Identification And Characterization Of Barrier Insulator Activity In The T-Cell Receptor Alpha Locus Control Region, Gayathri Devi Raghupathy

All Dissertations, Theses, and Capstone Projects

Genes of different spatiotemporal expression profiles are often juxtaposed in the genome. This organization raises risks of cross-regulatory influences from neighboring genes; for instance heterochromatin can spread over euchromatin or long-range acting enhancers can inappropriately activate genes. Gene regulatory elements such as Locus Control Regions (LCR) and Insulators prevent such cross-communications and allow for normal gene expression patterns. In transgenic systems, LCRs limit influences from surrounding chromatin by providing site-of-integration independent and specific spatiotemporal expression upon a linked transgene. The field’s understanding of the ability of an LCR to overcome chromatin influences and allow site-of-integration independent expression is minimal ...


Industry Spotlight: Medical Devices, Evan D. Poff 2019 Brigham Young University

Industry Spotlight: Medical Devices, Evan D. Poff

Marriott Student Review

Medical devices restore and even redefine health. This Industry Spotlight examines pre-market barriers, medtech business model quirks, current and future developments in the field, and the present-day move to value-based care in the medical device industry.


Characterization And Optimization Of Parylene-C Deposition Process Using Scs Parylene Coater, Hannah Hastings, Eric D. Johnston, Gyuseok Kim 2019 Singh Center for Nanotechnology

Characterization And Optimization Of Parylene-C Deposition Process Using Scs Parylene Coater, Hannah Hastings, Eric D. Johnston, Gyuseok Kim

Tool Data

Parylene-C has been deposited on bare Si wafers by physical vapor deposition using the SCS Coating Systems. Results show a 12 µm thick Parylene-C film with 10 g of dimer and negligible thickness variation across a wafer. We find a positive linear relationship between film thickness and mass of dimer at a range of 1 g to 18 g. However, the Al boat for dimer was burnt with 18 g of dimer, suggesting multiple depositions with 1 g to 10 g of dimer are recommended to achieve the Parylene-C film thicker than 12 µm.


Strain-Specific Protein Interaction And Localization Of Two Strains Of Potato Yellow Dwarf Virus And Functional Domains Of Their Matrix Protein, Chanyong Jang 2019 University of Kentucky

Strain-Specific Protein Interaction And Localization Of Two Strains Of Potato Yellow Dwarf Virus And Functional Domains Of Their Matrix Protein, Chanyong Jang

Theses and Dissertations--Plant Pathology

Potato yellow dwarf virus (PYDV) is the type species of the genus nucleorhabdovirus which is typified by its nucleotropic characters of the members. The virus accomplishes its replication and morphogenesis in the nuclei of infected cells. Two strains, Constricta strain (CYDV) and Sanguinolenta strain (SYDV) have been described at the level of vector-specificity. CYDV is vectored by Agallia constricta and SYDV is transmitted by Aceratagllia sanguinolenta. The full-length genome of CYDV was sequenced. The 12,792 nt antisense genome encodes seven open reading frames in the order of, nucleocapsid protein (N), unknown protein (X), phosphoprotein (P), movement protein (Y), matrix ...


Mechanisms And Immunogenicity Of Nspef-Induced Cell Death In B16f10 Melanoma Tumors, Alessandra Rossi, Olga N. Pakhomova, Andrei G. Pakhomov, Samantha Weygandt, Anna A. Bulysheva, Len E. Murray, Peter A. Mollica, Claudia Muratori 2019 Old Dominion University

Mechanisms And Immunogenicity Of Nspef-Induced Cell Death In B16f10 Melanoma Tumors, Alessandra Rossi, Olga N. Pakhomova, Andrei G. Pakhomov, Samantha Weygandt, Anna A. Bulysheva, Len E. Murray, Peter A. Mollica, Claudia Muratori

Bioelectrics Publications

Accumulating data indicates that some cancer treatments can restore anticancer immunosurveillance through the induction of tumor immunogenic cell death (ICD). Nanosecond pulsed electric fields (nsPEF) have been shown to efficiently ablate melanoma tumors. In this study we investigated the mechanisms and immunogenicity of nsPEF-induced cell death in B16F10 melanoma tumors. Our data show that in vitro nsPEF (20-200, 200-ns pulses, 7 kV/cm, 2 Hz) caused a rapid dose-dependent cell death which was not accompanied by caspase activation or PARP cleavage. The lack of nsPEF-induced apoptosis was confirmed in vivo in B16F10 tumors. NsPEF also failed to trigger ICD-linked responses ...


The Small Rna Teg41 Regulates Expression Of The Alpha Phenol-Soluble Modulins And Is Required For Virulence In Staphylococcus Aureus, Rachel L. Zapf, Richard E. Wiemels, Rebecca A. Keogh, Donald L. Holzschu, Kayla M. Howell, Emily Trzeciak, Andrew R. Caillet, Kellie A. King, Samantha A. Selhorst, Michael J. Naldrett, Jeffrey L. Bose, Ronan K. Carroll 2019 Ohio University

The Small Rna Teg41 Regulates Expression Of The Alpha Phenol-Soluble Modulins And Is Required For Virulence In Staphylococcus Aureus, Rachel L. Zapf, Richard E. Wiemels, Rebecca A. Keogh, Donald L. Holzschu, Kayla M. Howell, Emily Trzeciak, Andrew R. Caillet, Kellie A. King, Samantha A. Selhorst, Michael J. Naldrett, Jeffrey L. Bose, Ronan K. Carroll

Papers from the Nebraska Center for Biotechnology

Small RNAs (sRNAs) remain an understudied class of regulatory molecules in bacteria in general and in Gram-positive bacteria in particular. In the major human pathogen Staphylococcus aureus, hundreds of sRNAs have been identified; however, only a few have been characterized in detail. In this study, we investigate the role of the sRNA Teg41 in S. aureus virulence. We demonstrate that Teg41, an sRNA divergently transcribed from the locus that encodes the cytolytic alpha phenolsoluble modulin (αPSM) peptides, plays a critical role in αPSM production. Overproduction of Teg41 leads to an increase in αPSM levels and a corresponding increase in hemolytic ...


The Ethics Of Big Data In Genomics: The Instructive Icelandic Saga Of The Incidentalome, Donna M. Gitter 2019 Baruch College, Zicklin School of Business, City University of New York

The Ethics Of Big Data In Genomics: The Instructive Icelandic Saga Of The Incidentalome, Donna M. Gitter

Washington University Global Studies Law Review

DeCODE Genetics, Inc., a pioneering Icelandic biotech firm, recently introduced a free website that permits Icelanders to learn whether they carry mutations in the BRCA2 gene that are known to increase cancer risk, even if these citizens have never participated in genetic testing. Approximately five thousand Icelanders have elected thus far to receive their status. This site is made possible by the consanguinity of Icelandic citizens, who number fewer than 350,000, and their detailed genealogical records dating back centuries, a set of circumstances that presents a unique opportunity to study genetic mutations and the medical disorders associated with them ...


Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle Howell, Karin van Dijk, Christine S. Booth, Tomáš Helikar, Brain A. Couch, Rebecca Roston 2019 University of Nebraska - Lincoln

Visualizing The Invisible: A Guide To Designing, Printing, And Incorporating Dynamic 3d Molecular Models To Teach Structure–Function Relationships, Michelle Howell, Karin Van Dijk, Christine S. Booth, Tomáš Helikar, Brain A. Couch, Rebecca Roston

Biochemistry -- Faculty Publications

Understanding the intricate relationship between macromolecular structure and function represents a central goal of undergraduate biology education (1–3). In teaching complex three-dimensional (3D) concepts, instructors typically depend on static two-dimensional (2D) textbook images or computer-based visualization software, which can lead to unintended misconceptions (4–6). While chemical and molecular kits exist, these models cannot handle the size and detail of macromolecules. Consequently, students may graduate in the life sciences without understanding how structure underlies function or acquiring skills to translate between 2D and 3D molecular models (5, 7). Building on recent technological advances, 3D printing (3DP) potentiates an era ...


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