Biotechnology Commons^™

Loop-Ligation Of Dna Nanoswitch For Sensitivity Increase, Lillie Carnell

CURCE Annual Undergraduate Conference

DNA nanoswitches are tools to detect nucleic acids such as microRNAs and viral RNAs. The DNA nanoswitch is a linear duplex structure created from single-stranded circular viral M13 DNA using a DNA origami approach. Each nanoswitch can be designed to have explicit detector strands that bind to a specific DNA sequence. In the presence of a particular target sequence, the DNA nanoswitch will undergo a conformational change in which it switches from a linear “off” state to a looped “on” state. The shape of the DNA nanoswitch can then be detected using standard gel electrophoresis, a cheap and simple test. …

In Vitro Propagation Of A Critically Endangered African Violets (Saintpaulia Rupicola B.L. Burtt), Thomas W. Lowry Iii

Masters Theses, 2010-2019

The in vitro propagation is a promising method for the production of plants in species that are endangered, commercially valuable, and/or otherwise difficult to propagate through traditional horticultural methods. Leaf and petiole explants of critically endangered African violets (Saintpaulia rupicola B.L. Burtt) were cultured on a chemically defined medium that was supplemented with six different concentrations of thidiazuron (TDZ). The concentrations were used for either an induction medium on which the explants remained throughout development, or an induction medium on which the explants remained for 10 days followed by a basal growth medium for the remainder of the 12 …

Examining The Effect Of Interstitial Space On Eastern Oysters (Crassostrea Virginica): Applications Of Photogrammetry And Three-Dimensional Modeling, Bailie Lavan

Masters Theses, 2010-2019

Global oyster populations have decreased by as much as 99% in the past century. Oysters are known ecosystem engineers, providing benthic habitat for macrofauna, linking benthic and pelagic food webs, improving water quality, and mitigating shoreline erosion. Restoration efforts are critical in re-establishing native oyster populations. In the Chesapeake Bay, where oyster loss is primarily due to severe over harvest, artificial substrates with geometric shapes are widely used in restoration efforts. However, natural oyster reefs form emergent shapes with a high degree of aggregation and many interstitial spaces (three-dimensional volumetric spaces between oysters within a reef). The lack of interstitial …

A Machine Learning Technology For Rapid Detection Of Carbon Nanotubes/Dna Hybridization In Biosensor Healthcare Applications, Steven K. Ang

Master's Theses

In molecular biology, the term “DNA hybridization” generally refers to the process of forming a double stranded nucleic acid from joining two complementary strands of DNA. The degree of genetic similarity of the DNA resulting from hybridization can be detected ei ther by using the chemical characteristics of DNA samples or by utilizing reliable biosensors which transform the chemical characteristics into a source of electrical measurements. In past research about such sensors, known as DNA Hybridization Detection Systems, the thermal and electrical characteristics of carbon nanotubes are utilized to detect whether hybridization takes place or not. However, human interpretation of …

Molecular Determinants Of Ubqln2 Liquid-Liquid Phase Separation Modulated By Ubiquitin, Christine Habjan

Renée Crown University Honors Thesis Projects - All

Liquid-liquid phase separation (LLPS), the mechanism by which macromolecules demix to form a dense liquid- like phase in equilibrium with a phase dilute of molecules, is hypothesized to be the dominant mechanism governing membraneless organelle formation inside the cell. Stress granules, a type of membraneless organelle that assemble reversibly in response to cellular stress, may be formed through LLPS. Dysregulation of this process may lead to disease aggregates in vivo. LLPS is thought to be governed by the occurrence of weak, multivalent interactions between molecules such as proteins and RNA molecules. Multivalent interactions, the proposed driving force governing LLPS, are …

Zika Virus-Induced Lysis Of Cervical Cancer Cells, Harini Krishnapura

Electronic Theses and Dissertations

Cervical cancer is the fourth most frequent cancer in women with an estimated 570,000 new cases globally in 2018. Treatment of advanced cervical cancer is often unsuccessful leading to high cancer-related mortality rates, especially in under-resourced countries. Recently, a possible role for the cell surface glycoprotein CD24 in host cell specificity of Zika virus was reported. As an extension of this work, Zika viruses have been proposed as oncolytic therapy for the treatment of neuroblastoma and other CD24 positive tumors. To determine the permissiveness of cervical cancer cells to Zika virus infection and its association with CD24, we assessed cytopathic …

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 …

Development Of A Lectin-Fc Fusion Protein With Antiviral And Anti-Cancer Activity., Matthew William Dent

Electronic Theses and Dissertations

This thesis describes the development of a novel lectin-Fc fusion protein and its antiviral and anti-cancer activity. The molecule, Avaren-Fc (AvFc), is a fusion of a variant of the actinomycete lectin actinohivin (Avaren) and the Fc region of human IgG1, and is selective for the terminal α1,2-mannose residues found at the ends of high-mannose-type glycans that can be found on the surface of certain heavily glycosylated viruses and cancer cells. Here, AvFc was found to be able to neutralize simian immunodeficiency virus as well as Hepatitis C virus with nanomolar IC₅₀ values. Furthermore, AvFc recognizes a number of cell …

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

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 the end.

The Role Of Parathyroid Hormone 1 Receptor (Pth1r) Signaling In Gastric Epithelial Homeostasis, Maram Maher Al-Hasan

Theses

In the stomach, the epithelial stem cells are responsible for glandular homeostasis. These stem cells continuously undergo cellular proliferation and differentiation to balance the death of senescent cells. Studies conducted on gastric cancers showed a significant increase in parathyroid hormone-like hormone (PTHLH). Moreover, both PTHLH along with parathyroid hormone (PTH) act as endogenous ligands for parathyroid hormone 1 receptor (PTH1R) which belongs to family B of G- protein-coupled receptors (GPCRs). This receptor functions by mediating many different signaling pathways and the most studied pathway is the stimulation of cyclic adenosine monophosphate (cAMP) as a second messenger.

There are very few …

Multimodality Somatostatin Analog For Fluorescence-Guided Surgery In Cancer, Servando Hernandez Vargas

Dissertations and Theses (Open Access)

Cancer surgery remains the primary curative treatment for most solid cancers and has major therapeutic implications for patients with neuroendocrine tumors (NETs). Anatomical and functional imaging technologies are widely used during the pre- and postoperative stages, but intraoperative disease recognition relies on direct visual inspection and the hands of surgeons. The limited number of clinical tools for real-time intraoperative visual feedback restricts the ability to remove the complete cancer source and is partially responsible for the high rate of disease recurrence in patients. Intraoperative imaging with fluorescent contrast agents has the potential to improve the ability of surgeons to detect …

The Characterization Of T-Cell Manufacturing For Adoptive T-Cell Therapies, Amir Alpert

Dissertations and Theses (Open Access)

Adoptive T-cell therapy using genetically modified T cells has emerged as a potential therapeutic option for several malignancies. Central to the production of the cellular therapy is the manufacturing using a stimulation, genetic engineering, and expansion methodology. Within this framework, there is a delicate balance between expansion of the cells to a therapeutically relevant dosage and the need to retain the proliferative potential of the ‘living drug’. I show that as T-cells are expanded for elongated periods of time, they lose their proliferative potential and become functionally senescent despite the presence of multiple proliferative cytokines. In addition, I show that …

Analysis Of Barite Concrete As A Potential Neutron Radiation Shielding Material For Bnct Facilities, Murtafi'atin Rini, Widarto Widarto, Susilo Susilo, Made Dharma Putra Ngurah

ASEAN Journal on Science and Technology for Development

This research aimed to determine the potential of barite concrete as a neutron radiation shielding material in the development of boron neutron capture therapy, by obtaining its neutron attenuation coefficient. Barite concrete samples were supplied by the Center of Accelerator Science and Technology in Yogyakarta, Indonesia. The experiment consisted of two parts, namely density analysis and determination of the neutron attenuation coefficient. For the latter, plutonium-beryllium was used as the neutron source, while a high purity germanium detector was used to measure the neutron radiation level. The results showed that barite concrete with a 2130 kg.m–3 density had a neutron …

Removal Of Heavy Metals From An Actual Small Scale Gold Mining Wastewater By Sorption Onto Cocopeat, Samaniego Jessie O., Tanchuling Maria Antonia N.

ASEAN Journal on Science and Technology for Development

Cocopeat, a by-product of coconut husk, was used as adsorbent material to remove mercury (Hg) and other heavy metals (As, Ba, Cd, Pb) from the wastewater gathered from the tailings collection tank of a ball mill facility at the small scale gold mining (SSGM) area in Camarines Norte province, Philippines. Batch sorption tests were carried out using actual wastewater samples with reduced suspended solids collected after 60 min of settling and without modifying the pH and other parameters to simulate the actual condition in the field. Batch tests of water samples with an initial pH of 7.30 and adsorbent dose …

Gamma Radiography Testing Of Collimators For Boron Neutron Capture Therapy, Simangunsong Deo Clinton Maranatha, Sardjono Yohannes, Setyahandana Budi, Santosa Sigit, Nurjaman Fajar

ASEAN Journal on Science and Technology for Development

Boron neutron cancer therapy is a cancer treatment method that encompasses epithermal neutron irradiation of boron delivered to tumor cells. Using collimators, fast neutrons are moderated into epithermal neutrons. When radiation is performed, neutron beams are emitted and filtered by a collimator. In this study, 12 collimators used in the BNCT process were inspected for their quality, in terms of defects or flaws. The inspected collimators were manufactured by centrifugal casting and were composed of 99% pure nickel. They had the following dimensions: height of 145 mm, outer diameter of 190 mm, inner diameter of 160 mm, and thickness of …

Rockwell Hardness Testing Of Pure Nickel Collimators For Bnct Application, Prakasita Erasmus, Sardjono Yohanes, Setyahandana Budi

ASEAN Journal on Science and Technology for Development

In this study, Rockwell and Brinell hardness testing was used to examine material hardness. These methods were chosen because they are easy to carry out, relatively inexpensive, and almost all sizes and shapes can be tested, in which nickel hardness before and after centrifugal casting are identified and compared. These tests enable the determination of the hardness numbers of nickel collimators using for boron neutron capture therapy. The samples were five nickel plates with a dimension of 4.5 × 4.5 cm and five collimators. The collimators were cylindrical and made using centrifugal casting. The basic principle of the hardness test …

Feed Supplementation With Encapsulated Indigenous Probiotic Lactic Acid Bacteria Increased Broiler Chicken Performance, Pradipta Monica Sonia Indri, Harimurti Sri, Widodo Widodo

ASEAN Journal on Science and Technology for Development

The oral application of probiotics in the poultry industry is time-consuming and laborious. Therefore, using a powdered probiotic supplement that can easily mix with feed is important. We investigated the effect of spray drying encapsulation on the viability of indigenous probiotic lactic acid bacteria during production and storage and evaluated broiler chicken performance after providing the supplement. Encapsulated probiotics exhibited >80% survival rates after spray drying. All bacterial species maintained up to 80% cell viability rates after exposure to 80–85°C temperatures for 15 or 30 s. The viable cell number of all encapsulated bacteria decreased over seven weeks of storage. …

Characteristics In Water Phantom Of Epithermal Neutron Beam Produced By Double Layer Beam Shaping Assembly, Bilalodin Bilalodin, Suparta Gede Bayu, Hermanto Arief, Palupi Dwi Satya, Sardjono Yohannes

ASEAN Journal on Science and Technology for Development

A Double Layer Beam Shaping Assembly (DLBSA) was designed to produce epithermal neutrons for BNCT purposes. The Monte Carlo N-Particle eXtended program was used as the software to design the DLBSA and phantom. Distribution of epithermal neutron and gamma flux in the DLBSA and phantom and absorbed dose in the phantom were computed using the Particle and Heavy Ion Transport code System program. Testing results of epithermal neutron beam irradiation of the water phantom showed that epithermal neutrons were thermalized and penetrated the phantom up to a depth of 12 cm. The maximum value of the absorbed dose was 2 …

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 Research

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 …

Pengaruh Perlakuan Ethyl Methanesulphonate Terhadap Perkecambahan Dan Pertumbuhan Kentang Granola (Biji), Hanifah Nuraeni Suteja, Neni Rostini, Suseno Amien

Jurnal Kultivasi

Tujuan penelitian adalah mengevaluasi pengaruh ethyl methanesulphonate (EMS) terhadap pertumbuhan tanaman kentang Granola dari biji botani dan memperoleh konsentrasi efektif untuk mendapatkan mutan berdaya hasil tinggi. Percobaan dilakukan dalam dua tahap. Tahap pertama dilakukan di laboratorium kultur jaringan BALITSA, Lembang, yang terdiri dari tahap perlakuan EMS pada biji dengan konsentrasi 0,01%; 0,03%; 0,05%; 0,07%; 0,10%; 0,13%; 0,15%; 0,17%; dan 0,20%; selama 3 dan 6 jam, penanaman biji pada media kultur MS, perbanyakan planlet dan pengamatan planlet. Tahap kedua dilakukan di rumah kasa di Pangalengan yang terdiri dari tahapan aklimatisasi menggunakan Rancangan Acak Kelompok dengan 14 perlakuan EMS yang diulang 3 …

Consistency Is Futile!: Selecting Phycoremediators For Consortia, Tori Spencer

BIO 410 Spring 2019 Research Papers

Bioremediation is the process by which organisms remove and transform toxic compounds in a contaminated source. This is a waste management technique currently used to clean up man-made contamination. Many organisms act as natural remediators; in the case of algae, they are called phycoremediators who perform phycoremediaton. The term algae encompasses a variety of taxonomic groups and their diversity is still being realized; there are over 44,000 named species of the 72,000 species that we have identified. Some estimates calculate that there are over 200,000 diatom species alone. This diversity continues to be difficult to organize, which is problematic for …

Evaluating The Therapeutic Potential Of Crocin Against Diethylnitrosamine Induced Experimental Hepatocellular Carcinoma In Rats, Basma Ali Mustafa Awad

Theses

Hepatocellular carcinoma (HCC) is the fifth most common type of cancer and the third cause of cancer-related death worldwide. Liver cancer is the result of repeated injuries to the liver triggered by different causes. Currently, sorafenib is the only drug U.S. Food and Drug Administration approved targeted therapy. Sorafenib, an oral multikinase inhibitor, which inhibits the proliferation of tumor cells and blocks angiogenesis. Sorafenib has been shown to treat early and mild HCC lesions and it helped increase the survival rates at one year, but for only 44% of patients. Chemotherapies are an important line of defense when it comes …

Streptococcus Agalactiae Strains With Chromosomal Deletions Evade Detection With Molecular Methods, Isabella A. Tickler, Fred C. Tenover, Scott Dewell, Victoria M. Le, Rachel N. Blackman, Richard V. Goering, Amy E. Rogers, Heather Piwonka, Brittney D. Jung-Hynes, Derrick J. Chen, Michael J. Loeffelholz, Devasena Gnanashanmugam, Ellen Jo Baron

Biology Faculty Publications

Surveillance of circulating microbial populations is critical for monitoring the performance of a molecular diagnostic test. In this study, we characterized 31 isolates of Streptococcus agalactiae (group B Streptococcus [GBS]) from several geographic locations in the United States and Ireland that contain deletions in or adjacent to the region of the chromosome that encodes the hemolysin gene cfb, the region targeted by the Xpert GBS and GBS LB assays. PCR-negative, culture-positive isolates were recognized during verification studies of the Xpert GBS assay in 12 laboratories between 2012 and 2018. Whole-genome sequencing of 15 GBS isolates from 11 laboratories revealed …

Microarray Analysis Identifies Potential Genes Associated With Botrytis Cinerea And Hormonal Stresses, Kenna Marie Whitley

Biology Theses

Biotic and abiotic stresses critically influence plant survival and growth; survival depends on the ability to correctly sense and react to their environment. Certain environmental stresses must be overcome through careful manipulation of internal levels, and of the resulting signaling cascades. Hormones signaling networks and the crosstalk among each respective hormone signaling pathway are principle for response mediation via transcriptional reprogramming or altered signaling pathways. The long-term objective is to determine how plants sense biotic stresses, and how hormone signaling networks control and direct plant responses to the fungal pathogen Botrytis cinerea. This research aims to identify commonly regulated genes …

A Study On Vitamin D Metabolic Genes Single Nucleotide Polymorphisms And Their Linkage In Adult Asthmatic Emiratis, Amneh Mohammad Al Mousa

Biology Theses

Vitamin D normal levels are vital to many biological processes including its classical role in calcium and phosphate homeostasis, and regulation of immune and non-immune cells. Vitamin D mediates its actions via the vitamin D receptor (VDR) which is expressed in most tissues of the body including the airway smooth muscle. Asthma is a syndrome of chronic inflammatory airway disease. There is a genetic and immunological link between vitamin D and asthma. In this study, we aim to investigate whether asthma and its severity were associated with single nucleotide polymorphisms (SNPs) in vitamin D metabolic genes as well as vitamin …

Study Of Autosomal Str Markers In United Arab Emirates Population, Mohammed Naji Mohammed

Biology Theses

A study of the United Arab Emirates (UAE) population is important due to high consanguineous marriage, which may affect the power of discrimination of some loci. The genetic polymorphisms of 23 autosomal short tandem repeat (STR) loci including D3S1358, vWA, D16S539, CSF1PO, TPOX, D8S1179, D21S11, D18S51, D2S441, D19S433, TH01, FGA, D22S1045, D5S818, D13S317, D7S820, D10S1248, D1S1656, D12S391, D2S1338, D6S1043, Penta D and Penta E were evaluated in 571 random unrelated UAE Arabs population. Blood samples were collected on FTA cards. Targeted loci were amplified using Verifiler Express PCR Amplification Kit. PCR products were run on the ABI 3500 Genetic analyzer. …

Study Of Insertion-Deletion Polymorphisms (Indels) In The Uae Population, Maryam M. Matar Almheiri

Biology Theses

Insertion-deletion polymorphisms (indels) have been used less in forensic identification of individuals in comparison to short tandem repeat (STR) and single nucleotide polymorphism (SNP) systems. The use of indels has many advantages including low costs, simple typing methods as well as a small amplicon size of under 160 bp making them suitable for genotyping highly degraded DNA. They can also be valuable as a complementary tool to help resolve kinship cases, with the advantage of lower mutation rates when compared to STRs.

The main objective of this study was to investigate the polymorphism of 30 indel loci in the UAE …

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 engineer …

Interfacial Stress In The Development Of Biologics: Fundamental Understanding, Current Practice, And Future Perspective, Jinjiang Li, Mary E. Krause, Xiaodong Cheng, Yuan Cheng, Weiguo Dai, John J. Hill, Min Huang, Susan Jordan, Daniel Lacasse, Linda Narhi, Evgenyi Shalaev, Ian C. Shieh, Justin C. Thomas, Raymond Tu, Songyan Zheng, Lily Zhu

Publications and Research

Biologic products encounter various types of interfacial stress during development, manufacturing, and clinical administration. When proteins come in contact with vapor–liquid, solid–liquid, and liquid–liquid surfaces, these interfaces can significantly impact the protein drug product quality attributes, including formation of visible particles, subvisible particles, or soluble aggregates, or changes in target protein concentration due to adsorption of the molecule to various interfaces. Protein aggregation at interfaces is often accompanied by changes in conformation, as proteins modify their higher order structure in response to interfacial stresses such as hydrophobicity, charge, and mechanical stress. Formation of aggregates may elicit immunogenicity concerns; therefore, it …

Unified Methods For Feature Selection In Large-Scale Genomic Studies With Censored Survival Outcomes, Lauren Spirko-Burns, Karthik Devarajan

COBRA Preprint Series

One of the major goals in large-scale genomic studies is to identify genes with a prognostic impact on time-to-event outcomes which provide insight into the disease's process. With rapid developments in high-throughput genomic technologies in the past two decades, the scientific community is able to monitor the expression levels of tens of thousands of genes and proteins resulting in enormous data sets where the number of genomic features is far greater than the number of subjects. Methods based on univariate Cox regression are often used to select genomic features related to survival outcome; however, the Cox model assumes proportional hazards …